2WM5

X-ray structure of the substrate-free Mycobacterium tuberculosis cytochrome P450 CYP124


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE STRUCTURE (SEE REMARK BELOW)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.81% PEG MME, 0.1 M SODIUM CACODILATE, PH 6.8, 0.9 M SUCCINIC ACID
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.277α = 90
b = 74.006β = 103.13
c = 58.589γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rMIRRORS2009-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.569.31000.0610.439297417.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5489.70.431.72.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN-HOUSE STRUCTURE (SEE REMARK BELOW)1.569.3488311466298.240.15330.151990.17834RANDOM17.761
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]
-0.12-0.290.39-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.737
r_dihedral_angle_4_deg13.643
r_sphericity_free13.48
r_dihedral_angle_3_deg11.129
r_sphericity_bonded7.937
r_scangle_it6.93
r_dihedral_angle_1_deg5.859
r_scbond_it5.009
r_mcangle_it3.473
r_rigid_bond_restr3.028
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.737
r_dihedral_angle_4_deg13.643
r_sphericity_free13.48
r_dihedral_angle_3_deg11.129
r_sphericity_bonded7.937
r_scangle_it6.93
r_dihedral_angle_1_deg5.859
r_scbond_it5.009
r_mcangle_it3.473
r_rigid_bond_restr3.028
r_mcbond_it2.474
r_angle_refined_deg1.955
r_chiral_restr0.165
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3334
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing