2XBK
X-ray structure of the substrate-bound cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2X9P | PDB ENTRY 2X9P |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 296 | 0.2 M SODIUM MALONATE, PH 7.0; 20% PEG 3330, T=23 C |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.92 | α = 90 |
b = 99.69 | β = 111.92 |
c = 58.505 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 110 | CCD | ADSC QUANTUM 315 | MIRRORS | 2009-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.95 | 17.01 | 99.8 | 0.07 | 10 | 4.1 | 38650 | 1.5 | 30.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2.06 | 100 | 0.52 | 2.3 | 4.1 |
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 | PDB ENTRY 2X9P | 1.95 | 67.88 | 36749 | 1912 | 99.78 | 0.15286 | 0.14977 | 0.21396 | RANDOM | 30.816 |
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] | |
0.89 | -0.12 | -0.09 | -0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.616 |
r_dihedral_angle_4_deg | 20.808 |
r_dihedral_angle_3_deg | 14.959 |
r_scangle_it | 7.359 |
r_dihedral_angle_1_deg | 5.267 |
r_scbond_it | 5.052 |
r_mcangle_it | 2.975 |
r_rigid_bond_restr | 2.777 |
r_angle_refined_deg | 1.985 |
r_mcbond_it | 1.896 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3006 |
Nucleic Acid Atoms | |
Solvent Atoms | 272 |
Heterogen Atoms | 89 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |