4QDC

Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with FE2/S2 (INORGANIC) CLUSTER


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.22940.8 M NaH2PO4, 0.2 M K2HPO4, 2% PEG-3000, 20 mM CHES, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
4.0369.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.183α = 90
b = 162.183β = 90
c = 46.969γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRayonix MX300HE CCD X-ray detectormirrors2012-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.92CLSI08B1-1

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
11.944.5488.10.124189.349275
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)
11.91.9445.90.01327.91620

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 REPLACEMENTTHROUGHOUT2zyl1.9140.4549074245987.440.18820.18660.217RANDOM30.161
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]
0.260.130.26-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg13.07
r_dihedral_angle_1_deg6.985
r_mcangle_it5.329
r_mcbond_it4.17
r_mcbond_other4.162
r_angle_refined_deg1.68
r_angle_other_deg0.816
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg13.07
r_dihedral_angle_1_deg6.985
r_mcangle_it5.329
r_mcbond_it4.17
r_mcbond_other4.162
r_angle_refined_deg1.68
r_angle_other_deg0.816
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms50

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
XDSdata reduction