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Crystal Structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and genistein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 30% (W/v) PEG 2000 MME,
0.1M KCNS, 5 mM NADP
Crystals soaked for 24 hours in:
30% (W/v) PEG 2000 MME,
0.1M KCNS, 1 mM NADP, 5% (V/V) DMSO, 2 mM genistein
, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.37 α = 90 b = 113.89 β = 102.73 c = 69.4 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 PIXEL DECTRIS PILATUS 2M Platinum coated cylindrical mirror 2010-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 50 95.6 0.06 14.51 2.7 40171 40171 -3 32.9
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 2.45 94.9 0.247 4.84 2.52 6811
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 3QWI 2.3 46.7 38162 38162 2009 95.66 0.16102 0.16102 0.15903 0.1654 0.19881 0.2036 RANDOM 23.94
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] -0.95 -1.81 1.3 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_4_deg 9.141 r_dihedral_angle_1_deg 5.966 r_angle_refined_deg 1.391 r_angle_other_deg 1.193 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_4_deg 9.141 r_dihedral_angle_1_deg 5.966 r_angle_refined_deg 1.391 r_angle_other_deg 1.193 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7838 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 280
Software Software Software Name Purpose XRD1 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling