6L1B
Crystal Structure of P450BM3 with N-(3-cyclopentylpropanoyl)-L-pipecolyl-L-phenylalanine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5XA3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.9 | 293 | Tris-HCl, 0.1% (v/v) dimethyl sulfoxide, 0.1mM N-(3-cyclopentylpropanoyl)-L-pipecolyl-L-phenylalanine, MgCl, PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.854 | α = 90 |
b = 148.303 | β = 98.61 |
c = 63.691 | 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 EIGER R 4M | 2019-07-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.000 | SPring-8 | BL26B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.74 | 48 | 99.1 | 0.118 | 0.126 | 0.045 | 0.999 | 13.2 | 7.7 | 109197 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.74 | 1.77 | 98.1 | 1.591 | 1.704 | 0.609 | 0.517 | 7.7 |
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 | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5XA3 | 1.74 | 48 | 103701 | 5450 | 99.04 | 0.1734 | 0.1718 | 0.2029 | RANDOM | 22.927 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.562 |
r_dihedral_angle_4_deg | 16.521 |
r_dihedral_angle_3_deg | 13.809 |
r_dihedral_angle_1_deg | 6.99 |
r_angle_refined_deg | 1.638 |
r_angle_other_deg | 1.418 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7326 |
Nucleic Acid Atoms | |
Solvent Atoms | 545 |
Heterogen Atoms | 298 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |