2QBM
Crystal structure of the P450cam G248T mutant in the cyanide bound state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AKD | PDB entry 1akd |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 277 | 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.11 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 63.8 | ¦Á = 90 |
b = 64.6 | ¦Â = 90 |
c = 105.5 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARRESEARCH | DYNAMICALLY BENDABLE MIRROR | 2007-02-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.9796 | SLS | X10SA |
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 | 1.8 | 20 | 99 | 0.055 | 19.1 | 5.5 | 40676 | 40676 | -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) | |||||||||||
1.8 | 1.9 | 95 | 0.425 | 3.5 | 4.8 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 1akd | 1.8 | 19.94 | 40675 | 38641 | 2034 | 100 | 0.1785 | 0.17627 | 0.22045 | RANDOM | 24.505 |
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] | |
0.95 | 0.54 | -1.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.383 |
r_dihedral_angle_3_deg | 14.497 |
r_dihedral_angle_4_deg | 12.967 |
r_dihedral_angle_1_deg | 5.781 |
r_scangle_it | 3.946 |
r_scbond_it | 2.503 |
r_angle_refined_deg | 1.554 |
r_mcangle_it | 1.453 |
r_mcbond_it | 0.771 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3215 |
Nucleic Acid Atoms | |
Solvent Atoms | 416 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
XDS | data reduction |
XSCALE | data scaling |
CNS | phasing |