3HX8

Crystal structure of putative ketosteroid isomerase (NP_103587.1) from Mesorhizobium loti at 1.45 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627730.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.336α = 69.02
b = 55.111β = 76.89
c = 56.862γ = 64.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2009-03-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91162,0.97929,0.97915SSRLBL9-2

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
11.4528.02894.50.0419.0583844-318.22
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)
1.451.587.80.4521.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.4528.02883844421495.420.1490.1470.186RANDOM23.576
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]
-0.680.490.040.6-0.670.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.561
r_dihedral_angle_4_deg24.316
r_dihedral_angle_3_deg13.321
r_sphericity_free8.187
r_dihedral_angle_1_deg6.124
r_scangle_it5.076
r_sphericity_bonded3.684
r_scbond_it3.504
r_mcangle_it2.487
r_rigid_bond_restr1.599
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.561
r_dihedral_angle_4_deg24.316
r_dihedral_angle_3_deg13.321
r_sphericity_free8.187
r_dihedral_angle_1_deg6.124
r_scangle_it5.076
r_sphericity_bonded3.684
r_scbond_it3.504
r_mcangle_it2.487
r_rigid_bond_restr1.599
r_mcbond_it1.581
r_angle_refined_deg1.524
r_angle_other_deg0.888
r_mcbond_other0.692
r_chiral_restr0.094
r_bond_refined_d0.016
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 Atoms4034
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing