3IW0

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IVYPDB entry 3IVY

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