XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 6ME5 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | LIPIDIC CUBIC PHASE | | 293 | 60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol. |
Crystal Properties |
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Matthews coefficient | Solvent content |
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4.04 | 69.58 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 122.2 | α = 90 |
b = 122.2 | β = 90 |
c = 122.6 | γ = 90 |
Symmetry |
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Space Group | P 4 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | CS-PAD CXI-1 | | 2018-11-05 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.33 | SLAC LCLS | CXI |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | injection |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | 35 (fs) | 120 | 1.5 | 9.5 (KeV) | |
Data Reduction |
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Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
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1 | 65260 | 87453 | 65260 | |
Injection |
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
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1 | | 0.2 (µl/min) | undefined (µm) | | | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 3.3 | 30 | 100 | 0.998 | 0.119 | 8.5 | 1663 | | 14561 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 3.3 | 3.39 | | | 0.163 | 3.44 | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6me5 | 3.3 | 30 | 13778 | 728 | 99.75 | 0.2609 | 0.2585 | 0.3075 | RANDOM | 114.238 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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-2.39 | | | -2.39 | | 4.79 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.6 |
r_dihedral_angle_3_deg | 14.772 |
r_dihedral_angle_4_deg | 12.841 |
r_dihedral_angle_1_deg | 5.832 |
r_angle_refined_deg | 1.109 |
r_angle_other_deg | 0.907 |
r_chiral_restr | 0.059 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 33.6 |
r_dihedral_angle_3_deg | 14.772 |
r_dihedral_angle_4_deg | 12.841 |
r_dihedral_angle_1_deg | 5.832 |
r_angle_refined_deg | 1.109 |
r_angle_other_deg | 0.907 |
r_chiral_restr | 0.059 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 3648 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 23 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
PHASER | phasing |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |