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Crystal structure of ketosteroid isomerase Y14AY55FD99A from Pseudomonas testosteroni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 2.0 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.227 α = 90 b = 64.227 β = 90 c = 496.554 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 2011-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 38.196 99.5 0.077 21.9 10.5 22525 22525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 97 0.011 1.116 0.7 6.8 3061
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3M8C 2.5 35.05 22369 22369 1145 99.44 0.2416 0.2416 0.2386 0.3001 0.2571 RANDOM 62.921
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] 3.43 1.72 3.43 -5.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.349 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_4_deg 16.636 r_dihedral_angle_1_deg 6.296 r_scangle_it 2.186 r_scbond_it 1.332 r_angle_refined_deg 1.33 r_angle_other_deg 0.818 r_mcangle_it 0.777 r_mcbond_it 0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.349 r_dihedral_angle_3_deg 18.19 r_dihedral_angle_4_deg 16.636 r_dihedral_angle_1_deg 6.296 r_scangle_it 2.186 r_scbond_it 1.332 r_angle_refined_deg 1.33 r_angle_other_deg 0.818 r_mcangle_it 0.777 r_mcbond_it 0.419 r_mcbond_other 0.089 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3708 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 45
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction