3R4X
Crystal structure of bovine lactoperoxidase complexed with pyrazine-2-carboxamide at 2 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GC1 | PDB ENTRY 3GC1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.8 | 298 | Ammonium Iodide, PEG3350, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K , pH 6.8 , temperature 298 K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.924 | α = 90 |
b = 79.717 | β = 102.22 |
c = 77.005 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 77 | CCD | MARRESEARCH | MIRROR | 2010-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 2 | 75.26 | 96 | 0.087 | 30 | 39474 | 23.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.01 | 2.06 | 90.5 | 0.42 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3GC1 | 2.01 | 75.26 | 39474 | 39474 | 2104 | 97.8 | 0.213 | 0.21 | 0.256 | RANDOM | 36.34 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-1.83 | -0.12 | -2.57 | 4.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.286 |
r_dihedral_angle_4_deg | 16.939 |
r_dihedral_angle_3_deg | 13.662 |
r_dihedral_angle_1_deg | 2.511 |
r_angle_refined_deg | 2.185 |
r_mcangle_it | 1.997 |
r_scangle_it | 1.89 |
r_scbond_it | 1.513 |
r_mcbond_it | 1.177 |
r_chiral_restr | 0.184 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4774 |
Nucleic Acid Atoms | |
Solvent Atoms | 499 |
Heterogen Atoms | 195 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |