2XN8

X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X5LPDB ENTRY 2X5L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52772.0M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5, 4 DEG. CELSIUS
Crystal Properties
Matthews coefficientSolvent content
1.9537

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.365α = 90
b = 76.316β = 90
c = 90.357γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2010-04-24MSINGLE 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
11.6415.53990.1496.1463491.514.6
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)
11.641.7394.30.372.23.3

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 2X5L1.6458.343947233398.940.144060.140590.21003RANDOM15.975
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]
-0.150.79-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.64
r_dihedral_angle_4_deg14.427
r_dihedral_angle_3_deg13.446
r_scangle_it6.743
r_dihedral_angle_1_deg6.227
r_scbond_it4.862
r_mcangle_it3.044
r_rigid_bond_restr2.575
r_mcbond_it2.02
r_angle_refined_deg1.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.64
r_dihedral_angle_4_deg14.427
r_dihedral_angle_3_deg13.446
r_scangle_it6.743
r_dihedral_angle_1_deg6.227
r_scbond_it4.862
r_mcangle_it3.044
r_rigid_bond_restr2.575
r_mcbond_it2.02
r_angle_refined_deg1.834
r_chiral_restr0.15
r_bond_refined_d0.023
r_gen_planes_refined0.011
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3187
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing