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Crystal structure of the binary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Apo form) and coumestrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IS3 PDB ENTRY 3IS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris
Soaked for 24 hours with:
20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris
2 mM coumestrol.
5% DMSO in the soaking solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.92 α = 90 b = 67.92 β = 90 c = 267.65 γ = 90
Symmetry Space Group I 41 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 PIXEL DECTRIS PILATUS 2M Platinum coated cylindrical mirror 2010-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.000 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 20 97.4 0.078 0.078 11.8 4.5 24719 24719 -3 24
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 1.9 1.94 82.7 3.2 0.203 3.2 2.5 1249
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3IS3 1.9 19.7 23482 23482 1236 97.39 0.15641 0.15641 0.1556 0.1696 0.17185 0.1779 RANDOM 32.813
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] 1.35 1.35 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.466 r_dihedral_angle_3_deg 11.982 r_dihedral_angle_4_deg 8.988 r_dihedral_angle_1_deg 6.106 r_angle_refined_deg 1.299 r_angle_other_deg 0.771 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.466 r_dihedral_angle_3_deg 11.982 r_dihedral_angle_4_deg 8.988 r_dihedral_angle_1_deg 6.106 r_angle_refined_deg 1.299 r_angle_other_deg 0.771 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 1964 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 55
Software Software Software Name Purpose XRD1 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling