7CL8

Testosterone-bound structure of CYP154C2 from Streptomyces avermitilis in an closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6L69 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.06 M Divalents, 0.1 M Buffer System 2 pH 7.5, 50% v/v Precipitant mix 1
Crystal Properties
Matthews coefficientSolvent content
2.5852.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 61.82β = 90
c = 133.77γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 225 mm CCD2019-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.425099.70.0780.99814.79.884407
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.599.60.4330.9234.9

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 REPLACEMENTTHROUGHOUT6L691.4241.9379964431699.460.14510.14420.1609RANDOM15.399
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.835
r_dihedral_angle_4_deg19.939
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.918
r_angle_refined_deg2.046
r_angle_other_deg1.634
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.835
r_dihedral_angle_4_deg19.939
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.918
r_angle_refined_deg2.046
r_angle_other_deg1.634
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3032
Nucleic Acid Atoms
Solvent Atoms640
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing