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Crystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and biochanin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QWI pdb entry 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,
5mM NADP,
Crystals soaked for 24 hours in:
30% (W/V) PEG 2000 MME,
0.1M KCNS,
1mM NADP,
5% (V/V) DMSO,
2 mM biochanin A , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.43 α = 90 b = 115.28 β = 102.93 c = 69.6 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 35 76.7 0.033 19 2.3 32695 32695 -3 39.2
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 2.36 50.1 0.212 6.63 2.27 1574
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 3QWI 2.5 33.43 25680 25680 1352 81.28 0.16853 0.16853 0.16641 0.1706 0.20801 0.2093 RANDOM 27.813
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] -1.64 -1.28 2.54 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.711 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_4_deg 10.602 r_dihedral_angle_1_deg 5.661 r_angle_refined_deg 1.406 r_angle_other_deg 1.237 r_chiral_restr 0.073 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 38.711 r_dihedral_angle_3_deg 14.533 r_dihedral_angle_4_deg 10.602 r_dihedral_angle_1_deg 5.661 r_angle_refined_deg 1.406 r_angle_other_deg 1.237 r_chiral_restr 0.073 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 7843 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 254
Software Software Software Name Purpose XRD1 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling