3FZW

Crystal Structure of Ketosteroid Isomerase D40N-D103N from Pseudomonas putida (pKSI) with bound equilenin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2INXPDB ENTRY 2INX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Ammonium sulphate 1.4 M, 2-propanol 6.5%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6854.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.876α = 90
b = 71.196β = 89.92
c = 50.452γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-24SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979462SSRLBL9-1

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
11.3250940.08810.3372.96814968149-3-311.7
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)
11.321.3770.20.3732.25090

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2INX1.3255.056813668136345293.760.1510.1510.1490.183RANDOM19.12
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]
1.560.51-0.24-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.728
r_dihedral_angle_4_deg20.791
r_dihedral_angle_3_deg13.931
r_sphericity_free8.979
r_dihedral_angle_1_deg5.8
r_sphericity_bonded5.089
r_scangle_it4.486
r_mcangle_it3.685
r_scbond_it3.355
r_mcbond_it3.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.728
r_dihedral_angle_4_deg20.791
r_dihedral_angle_3_deg13.931
r_sphericity_free8.979
r_dihedral_angle_1_deg5.8
r_sphericity_bonded5.089
r_scangle_it4.486
r_mcangle_it3.685
r_scbond_it3.355
r_mcbond_it3.016
r_rigid_bond_restr2.662
r_angle_refined_deg2.126
r_nbtor_refined0.325
r_symmetry_vdw_refined0.315
r_nbd_refined0.221
r_symmetry_hbond_refined0.195
r_xyhbond_nbd_refined0.165
r_chiral_restr0.153
r_bond_refined_d0.023
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1971
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection