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Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2% (V/V) PEG (POLYETHYLENE GLYCOL) 400, 0.1 M HEPES (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) BUFFER PH 7.5, 2.0 M AMMONIUM SULFATE. SITTING DROP. TEMPERATURE 293 K. THE PROTEIN SOLUTION SAMPLE WAS INCUBATED WITH 1,4-ANDROSTADIENE-3,17-DIONE POWDER ON ICE FOR 3 H PRIOR TO THE CRYSTALLIZATION EXPERIMENT.
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.747 α = 90 b = 132.142 β = 90 c = 363.597 γ = 90
Symmetry Space Group P 21 21 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 CCD 2011-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.3 49.42 99.5 0.13 7.2 4.6 229728
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 2.3 2.42 96.7 0.72 1.9 4.5
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 OTHER THROUGHOUT NONE 2.3 49.42 217960 11485 99.65 0.21236 0.21045 0.2144 0.24882 0.2517 RANDOM 41.418
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 0.03 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 5.667 r_angle_other_deg 2.743 r_angle_refined_deg 1.415 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_4_deg 19.837 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 5.667 r_angle_other_deg 2.743 r_angle_refined_deg 1.415 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 29620 Nucleic Acid Atoms Solvent Atoms 1414 Heterogen Atoms 674
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling