3M8C

Crystal Structure of Ketosteroid Isomerase D99N from Pseudomonas Testosteroni (tKSI) with Equilenin Bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8CHO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop7.22981.4 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8256.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.312α = 90
b = 64.312β = 90
c = 506.174γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-01-16SINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 325 mm CCD2010-01-06SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.98SSRLBL9-1
2SYNCHROTRONSSRL BEAMLINE BL9-20.98SSRLBL9-2

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
1,22.133.6399.20.09420.611.7380273802724.5
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)
2.12.2194.80.4164.98.15131

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT8CHO2.184.363802737837189599.150.1690.1690.1660.222RANDOM26.739
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]
1.020.511.02-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.228
r_dihedral_angle_4_deg20.81
r_dihedral_angle_3_deg15.56
r_dihedral_angle_1_deg6.551
r_scangle_it4.845
r_scbond_it3.223
r_mcangle_it2.018
r_angle_refined_deg1.989
r_mcbond_it1.17
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.228
r_dihedral_angle_4_deg20.81
r_dihedral_angle_3_deg15.56
r_dihedral_angle_1_deg6.551
r_scangle_it4.845
r_scbond_it3.223
r_mcangle_it2.018
r_angle_refined_deg1.989
r_mcbond_it1.17
r_chiral_restr0.146
r_bond_refined_d0.023
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3756
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Web-Icedata collection
Blu-Icedata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing