3KW4

Crystal structure of cytochrome 2B4 in complex with the anti-platelet drug ticlopidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SUOPDB ENTRY 1SUO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.529120% (w/v) PEG 8000, 0.2 M MgCl2 and 0.1 M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.1961.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.5α = 90
b = 93.5β = 90
c = 137.07γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6780.97399.80.1010.1014.97.220223
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.672.811000.4160.4161.77.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SUO2.6768.542460519135102899.60.1980.1950.253RANDOM67.3
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]
-5.735-5.73511.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.84
r_dihedral_angle_4_deg22.894
r_dihedral_angle_3_deg18.074
r_dihedral_angle_1_deg5.844
r_scangle_it4.317
r_scbond_it2.554
r_mcangle_it1.736
r_angle_refined_deg1.406
r_mcbond_it0.897
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.84
r_dihedral_angle_4_deg22.894
r_dihedral_angle_3_deg18.074
r_dihedral_angle_1_deg5.844
r_scangle_it4.317
r_scbond_it2.554
r_mcangle_it1.736
r_angle_refined_deg1.406
r_mcbond_it0.897
r_chiral_restr0.084
r_gen_planes_refined0.011
r_bond_refined_d0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3693
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms208

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction