3CPO

Crystal structure of ketosteroid isomerase D40N with bound 2-fluorophenol


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 5-7%, PROTEIN CONCENTRATION 25 MG/ML, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.347α = 90
b = 95.013β = 90
c = 72.376γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-01-01SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.97952SSRLBL9-1

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
11.245095.30.05314.711.33329633296-3
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)
1.241.2867.70.525.42335

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 2INX1.2436.193325333253166995.250.1680.1680.1660.2RANDOM22.999
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]
1.54-1.29-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.174
r_dihedral_angle_4_deg20.873
r_dihedral_angle_3_deg14.377
r_sphericity_free11.727
r_sphericity_bonded8.456
r_dihedral_angle_1_deg6.33
r_scangle_it5.398
r_mcangle_it4.924
r_scbond_it4.252
r_mcbond_it3.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.174
r_dihedral_angle_4_deg20.873
r_dihedral_angle_3_deg14.377
r_sphericity_free11.727
r_sphericity_bonded8.456
r_dihedral_angle_1_deg6.33
r_scangle_it5.398
r_mcangle_it4.924
r_scbond_it4.252
r_mcbond_it3.848
r_rigid_bond_restr3.049
r_angle_refined_deg1.945
r_nbtor_refined0.327
r_symmetry_vdw_refined0.252
r_nbd_refined0.233
r_xyhbond_nbd_refined0.212
r_symmetry_hbond_refined0.184
r_chiral_restr0.148
r_bond_refined_d0.022
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1048
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling