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Crystal structure of ketosteroid isomerase F54G from Pseudomonas testosteroni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8C PDB entry 3M8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 1.4 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.571 α = 90 b = 64.571 β = 90 c = 502.154 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2011-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.980 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.52 39.5 99.7 0.102 18.1 10.5 22617 43.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.66 98.1 0.408 4.2 7.1 3118
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3M8C 2.52 37.36 22472 22472 1147 99.72 0.2262 0.2262 0.224 0.2253 0.2679 0.2618 RANDOM 25.9096
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] 1.09 0.54 1.09 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_dihedral_angle_4_deg 18.428 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_1_deg 6.258 r_scangle_it 2.018 r_angle_refined_deg 1.286 r_scbond_it 1.219 r_angle_other_deg 0.835 r_mcangle_it 0.779 r_mcbond_it 0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.906 r_dihedral_angle_4_deg 18.428 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_1_deg 6.258 r_scangle_it 2.018 r_angle_refined_deg 1.286 r_scbond_it 1.219 r_angle_other_deg 0.835 r_mcangle_it 0.779 r_mcbond_it 0.413 r_chiral_restr 0.074 r_mcbond_other 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3728 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 70
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection Web-Ice data collection XDS data reduction SCALA data scaling