2WM4

X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP124 in complex with phytanic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WM5PDB ENTRY 2WM5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.521% PEG4000, 0.1 M BIS-TRIS, PH 5.5, 0.2 M CALCIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.1643.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.596α = 90
b = 73.4β = 90
c = 109.696γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315rMIRRORS2009-01-24MSINGLE 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
12.150970.0930.86.22478429.1
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)
12.12.1476.60.533.64

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WM52.1143.9422780119796.770.1690.165610.23189RANDOM29.366
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]
-2.161.980.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.94
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg16.844
r_sphericity_free8.668
r_dihedral_angle_1_deg6.878
r_scangle_it4.524
r_sphericity_bonded3.963
r_scbond_it3.055
r_rigid_bond_restr2.045
r_mcangle_it2.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.94
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg16.844
r_sphericity_free8.668
r_dihedral_angle_1_deg6.878
r_scangle_it4.524
r_sphericity_bonded3.963
r_scbond_it3.055
r_rigid_bond_restr2.045
r_mcangle_it2.002
r_angle_refined_deg1.907
r_mcbond_it1.231
r_chiral_restr0.145
r_bond_refined_d0.021
r_gen_planes_refined0.009
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 Atoms3346
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing