4HGG
Crystal structure of P450 BM3 5F5R heme domain variant complexed with styrene
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J4S | PDB ENTRY 2J4S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 100-160 mM magnesium chloride, 100 mM 2-(N-morpholino)ethanesulfonic acid (pH 6.5), 10-20% PEG 3350/PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.9 | α = 90 |
b = 147.98 | β = 98.37 |
c = 64.01 | 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2012-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.99 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.7 | 48.11 | 100 | 32.26 | 6.8 | 118652 | 118652 | 1 | -3 | 28.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.7 | 1.786 | 100 | 16367 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2J4S | 1.7 | 48.11 | 118652 | 118652 | 5933 | 99.96 | 0.18041 | 0.17881 | 0.21101 | RANDOM | 23.257 |
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] | |
-0.56 | -0.03 | 0.08 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.346 |
r_dihedral_angle_3_deg | 15.125 |
r_dihedral_angle_4_deg | 13.609 |
r_rigid_bond_restr | 13.03 |
r_dihedral_angle_1_deg | 6.343 |
r_angle_refined_deg | 2.533 |
r_chiral_restr | 0.224 |
r_bond_refined_d | 0.023 |
r_gen_planes_refined | 0.011 |
r_sphericity_free |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7062 |
Nucleic Acid Atoms | |
Solvent Atoms | 696 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
Auto-Rickshaw | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |