2INX

Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 2,6-difluorophenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B32PDB entry 2B32

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Ammonium sulphate 1.4 M, 2-propanol 6.5% protein concentration 25 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.114α = 90
b = 94.887β = 90
c = 72.424γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152004-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.900APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.547.496.80.07916.191991119274-324.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5596.70.3744.48.91890

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 2B321.547.418650183093.690.190.1850.234RANDOM26.929
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]
2.88-2.58-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.808
r_dihedral_angle_4_deg18.333
r_dihedral_angle_3_deg13.768
r_sphericity_free11.133
r_sphericity_bonded6.452
r_dihedral_angle_1_deg5.874
r_scangle_it5.5
r_scbond_it3.957
r_mcangle_it3.285
r_rigid_bond_restr2.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.808
r_dihedral_angle_4_deg18.333
r_dihedral_angle_3_deg13.768
r_sphericity_free11.133
r_sphericity_bonded6.452
r_dihedral_angle_1_deg5.874
r_scangle_it5.5
r_scbond_it3.957
r_mcangle_it3.285
r_rigid_bond_restr2.575
r_mcbond_it2.266
r_angle_refined_deg1.906
r_nbtor_refined0.317
r_symmetry_vdw_refined0.244
r_nbd_refined0.219
r_xyhbond_nbd_refined0.19
r_symmetry_hbond_refined0.174
r_chiral_restr0.13
r_bond_refined_d0.021
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1020
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing