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The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D4C PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY experimental model PDB 1E39 PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY experimental model PDB 1KF6 PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY experimental model PDB 1NEK PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY experimental model PDB 1ZOY PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.233 α = 90 b = 114.308 β = 90 c = 110.161 γ = 90
Symmetry Space Group C 2 2 21
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 210r MIRRORS 2007-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 1.6 49.6 97 0.08 22.6 11.1 80282 16
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 1.6 1.69 83.8 0.32 4.7 6.1
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 PDB ENTRIES 1D4C, 1E39, 1KF6, 1NEK, 1ZOY 1.6 39.65 75998 4019 96.94 0.15875 0.15786 0.1565 0.17539 0.175 RANDOM 16.802
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 15.35 r_dihedral_angle_3_deg 11.26 r_dihedral_angle_1_deg 5.367 r_angle_refined_deg 1.436 r_angle_other_deg 0.869 r_nbtor_refined 0.307 r_nbd_other 0.3 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 15.35 r_dihedral_angle_3_deg 11.26 r_dihedral_angle_1_deg 5.367 r_angle_refined_deg 1.436 r_angle_other_deg 0.869 r_nbtor_refined 0.307 r_nbd_other 0.3 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.225 r_nbtor_other 0.142 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3598 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing