3V8D

Crystal structure of human CYP7A1 in complex with 7-ketocholesterol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DAXpdb entry 3DAX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.629130% PEG-400, 0.2M lithium sulfate, 0.1M trisodium citrate, pH 5.6, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.618α = 66.33
b = 74.22β = 75.53
c = 87.933γ = 69.62
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97625CLSI08ID-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
11.95097.60.0749.63.892430
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)
11.91.9796.40.8483.79089

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 3DAX1.95092179206697.6010.1860.18520.225THIN SHELLS (SFTOOLS)26.151
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]
-0.613-0.549-0.2430.260.720.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.518
r_dihedral_angle_4_deg15.459
r_dihedral_angle_3_deg11.886
r_dihedral_angle_1_deg5.408
r_angle_refined_deg1.407
r_angle_other_deg0.808
r_chiral_restr0.061
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.518
r_dihedral_angle_4_deg15.459
r_dihedral_angle_3_deg11.886
r_dihedral_angle_1_deg5.408
r_angle_refined_deg1.407
r_angle_other_deg0.808
r_chiral_restr0.061
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7479
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms188

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling