3RN0
Crystal Structure of the W199K-MauG/pre-Methylamine Dehydrogenase Complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3L4M | PDB entry 3L4M |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | Drops contained 1uL protein with 2.5uL reservoir solution. Protein solution: 100uM W199K-MauG and 50uM preMADH in 10mM potassium phosphate, pH 7.5. Reservoir solution contained: 22% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.527 | α = 109.94 |
b = 83.524 | β = 91.54 |
c = 107.782 | γ = 105.78 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Biomorph mirrors (Kirkpatrick-Baez configuration) | 2010-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.03315 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | ||||||||
1 | 1.91 | 50 | 88.8 | 0.085 | 12.2 | 3.5 | 131689 | 116940 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.91 | 1.96 | 46.6 | 0.42 | 2 | 2.5 | 6532 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3L4M | 1.91 | 39.58 | 128503 | 111052 | 5868 | 86.42 | 0.17597 | 0.17312 | 0.19 | 0.22972 | 0.24 | RANDOM | 33.985 |
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] | |
0.02 | 0.09 | 0.01 | 0.18 | -0.13 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.677 |
r_dihedral_angle_4_deg | 17.625 |
r_dihedral_angle_3_deg | 15.448 |
r_dihedral_angle_1_deg | 7.116 |
r_scangle_it | 4.458 |
r_scbond_it | 3.098 |
r_angle_refined_deg | 2.178 |
r_mcangle_it | 1.732 |
r_mcbond_it | 1.113 |
r_chiral_restr | 0.169 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13221 |
Nucleic Acid Atoms | |
Solvent Atoms | 1180 |
Heterogen Atoms | 222 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |