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Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with FE2/S2 (INORGANIC) CLUSTER
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 294 0.8 M NaH2PO4, 0.2 M K2HPO4, 2% PEG-3000, 20 mM CHES, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 4.03 69.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.183 α = 90 b = 162.183 β = 90 c = 46.969 γ = 120
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 Rayonix MX300HE CCD X-ray detector mirrors 2012-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.92 CLSI 08B1-1
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 1.9 44.54 88.1 0.124 18 9.3 49275
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 1.9 1.94 45.9 0.013 2 7.9 1620
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2zyl 1.9 140.45 49074 2459 87.44 0.1882 0.1866 0.196 0.217 0.2292 RANDOM 30.161
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] 0.26 0.13 0.26 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_4_deg 18.778 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 6.985 r_mcangle_it 5.329 r_mcbond_it 4.17 r_mcbond_other 4.162 r_angle_refined_deg 1.68 r_angle_other_deg 0.816 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_4_deg 18.778 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 6.985 r_mcangle_it 5.329 r_mcbond_it 4.17 r_mcbond_other 4.162 r_angle_refined_deg 1.68 r_angle_other_deg 0.816 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 50
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxDC data collection XDS data reduction