3IW2

Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with econazole


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
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.632α = 90
b = 86.016β = 90
c = 89.455γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135mirrors2008-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.195094.220.0988.72180521805
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3IVY2.1949.632180521805117994.770.164970.161080.23745RANDOM15.764
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]
-0.080.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.945
r_dihedral_angle_4_deg15.704
r_dihedral_angle_3_deg14.456
r_dihedral_angle_1_deg8.818
r_scangle_it5.382
r_scbond_it3.875
r_mcangle_it2.195
r_angle_refined_deg1.866
r_mcbond_it1.62
r_angle_other_deg1.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.945
r_dihedral_angle_4_deg15.704
r_dihedral_angle_3_deg14.456
r_dihedral_angle_1_deg8.818
r_scangle_it5.382
r_scbond_it3.875
r_mcangle_it2.195
r_angle_refined_deg1.866
r_mcbond_it1.62
r_angle_other_deg1.237
r_mcbond_other0.608
r_xyhbond_nbd_other0.397
r_symmetry_hbond_refined0.334
r_nbd_refined0.265
r_xyhbond_nbd_refined0.229
r_nbd_other0.215
r_symmetry_vdw_other0.214
r_nbtor_refined0.185
r_symmetry_vdw_refined0.143
r_chiral_restr0.133
r_nbtor_other0.092
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3126
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing