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Crystal structure of hydroxysteroid dehydrogenase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FMC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 294 0.1 M HEPES:NaOH pH 7.5, 20% (w/v) PEG 4000, and 10% (v/v) 2-propanol
Crystal Properties Matthews coefficient Solvent content 1.94 36.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.829 α = 90 b = 100.188 β = 95.571 c = 160.219 γ = 90
Symmetry Space Group P 1 21 1
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 270 2019-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.7 50 98.7 0.98 16.7 3.6 50045
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.776
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1FMC 2.703 38.093 49980 2490 98.306 0.203 0.198 0.293 0.2726 58.994
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] -0.028 -0.014 0.019 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.914 r_dihedral_angle_3_deg 19.059 r_dihedral_angle_4_deg 16.272 r_lrange_it 10.916 r_lrange_other 10.915 r_dihedral_angle_1_deg 8.269 r_scangle_it 7.589 r_scangle_other 7.588 r_mcangle_it 7.563 r_mcangle_other 7.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.914 r_dihedral_angle_3_deg 19.059 r_dihedral_angle_4_deg 16.272 r_lrange_it 10.916 r_lrange_other 10.915 r_dihedral_angle_1_deg 8.269 r_scangle_it 7.589 r_scangle_other 7.588 r_mcangle_it 7.563 r_mcangle_other 7.562 r_mcbond_it 4.999 r_mcbond_other 4.99 r_scbond_it 4.928 r_scbond_other 4.928 r_angle_refined_deg 1.579 r_angle_other_deg 1.231 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.213 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.171 r_nbtor_refined 0.154 r_symmetry_nbd_refined 0.151 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.071 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14381 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing