3IW0

Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125, C2221 crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively., VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4449.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.5α = 90
b = 118.9β = 90
c = 145.9γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing2008-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.0000DiamondI03

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
11.73099.380.07316.44951149511
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)
11.71.899.80.4472.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3IVY1.729.374951149511268999.380.155950.155950.154130.18885RANDOM14.769
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]
0.260.89-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.816
r_dihedral_angle_4_deg15.673
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg5.627
r_scangle_it2.961
r_scbond_it2.109
r_angle_refined_deg1.281
r_mcangle_it1.258
r_angle_other_deg0.951
r_mcbond_it0.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.816
r_dihedral_angle_4_deg15.673
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg5.627
r_scangle_it2.961
r_scbond_it2.109
r_angle_refined_deg1.281
r_mcangle_it1.258
r_angle_other_deg0.951
r_mcbond_it0.932
r_symmetry_hbond_refined0.251
r_symmetry_vdw_refined0.249
r_nbd_refined0.233
r_symmetry_vdw_other0.224
r_mcbond_other0.208
r_nbd_other0.199
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.178
r_nbtor_other0.083
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3183
Nucleic Acid Atoms
Solvent Atoms698
Heterogen Atoms48

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling