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Crystal structure of the 17beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus in complex with NADPH and kaempferol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)
Crystals soaked in:
30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 2MM KAEMPFEROL, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.95 α = 90 b = 116.64 β = 102.54 c = 70.24 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 MAR CCD 165 mm PT-COATED TOROIDAL MIRROR 2008-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 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 2.61 39.1 93.9 0.061 0.061 12.5 3.5 28133 28133 -3 46
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 2.61 2.75 75.5 0.187 0.187 5 2.6 3279
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QWF 2.62 39.1 28102 28102 1410 94.3 0.17188 0.17188 0.168 0.24 0.2409 RANDOM 39.801
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] 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_3_deg 14.868 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_1_deg 5.651 r_scangle_it 1.664 r_angle_refined_deg 1.246 r_scbond_it 1 r_mcangle_it 0.625 r_mcbond_it 0.32 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.253 r_dihedral_angle_3_deg 14.868 r_dihedral_angle_4_deg 12.592 r_dihedral_angle_1_deg 5.651 r_scangle_it 1.664 r_angle_refined_deg 1.246 r_scbond_it 1 r_mcangle_it 0.625 r_mcbond_it 0.32 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7843 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 262
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling