2XC3

X-ray structure of Mycobacterium tuberculosis cyp125 bound to the reverse type I inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52772 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, PH 5.5, 0.5 M NACL, 4 DEG. CELSIUS
Crystal Properties
Matthews coefficientSolvent content
1.9236

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.356α = 90
b = 76.399β = 90
c = 90.407γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2010-02-04MSINGLE 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
11.55091.90.04267.1560931.514.1
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)
11.51.58630.147.54.3

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 2X5L1.546.5853185284091.860.124870.122090.17701RANDOM16.009
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]
-0.240.210.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.742
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg12.13
r_scangle_it6.848
r_dihedral_angle_1_deg5.88
r_scbond_it4.966
r_mcangle_it3.32
r_rigid_bond_restr2.643
r_mcbond_it2.28
r_angle_refined_deg1.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.742
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg12.13
r_scangle_it6.848
r_dihedral_angle_1_deg5.88
r_scbond_it4.966
r_mcangle_it3.32
r_rigid_bond_restr2.643
r_mcbond_it2.28
r_angle_refined_deg1.926
r_angle_other_deg1.387
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_gen_planes_other0.012
r_bond_other_d0.002
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 Atoms3193
Nucleic Acid Atoms
Solvent Atoms584
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing