2X5L

X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125, ALTERNATIVE 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, HANGING DROP5.52770.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS, PH 5.5, 17% PEG 10000 AT 4 C
Crystal Properties
Matthews coefficientSolvent content
2.1542.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.48α = 90
b = 74.578β = 90
c = 102.225γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDMIRRORS2010-01-15MSINGLE 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
11.48102.694.90.079.54.1666321.515
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)
11.481.5671.60.551.51.9

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 3IVY1.48102.2263143336794.730.153150.150520.20179RANDOM18.624
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]
0.20.14-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg13.093
r_sphericity_free10.468
r_sphericity_bonded6.721
r_scangle_it6.275
r_dihedral_angle_1_deg5.936
r_scbond_it4.542
r_mcangle_it3.095
r_rigid_bond_restr2.703
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.505
r_dihedral_angle_4_deg15.069
r_dihedral_angle_3_deg13.093
r_sphericity_free10.468
r_sphericity_bonded6.721
r_scangle_it6.275
r_dihedral_angle_1_deg5.936
r_scbond_it4.542
r_mcangle_it3.095
r_rigid_bond_restr2.703
r_mcbond_it2.182
r_angle_refined_deg1.97
r_chiral_restr0.171
r_bond_refined_d0.024
r_gen_planes_refined0.013
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 Atoms3259
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing