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Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with 1-{4-[(2-methyl-1-piperidinyl)sulfonyl]phenyl}-2-pyrrolidinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 20% PEG3350, 0.2 M sodium acetate, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.2 α = 90 b = 64.19 β = 90 c = 95.86 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 QUANTUM 315r 2010-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 1.97 53.34 99.9 0.092 5.2 25694 25694
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 1.97 2.08 99.9 0.35 4.5 5.1 3684
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 (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 2FGB 1.97 53.34 133034 24338 1306 99.91 0.16492 0.16295 0.1681 0.2015 0.2114 RANDOM 15.754
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] 0.12 0.61 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.283 r_dihedral_angle_4_deg 13.32 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_1_deg 6.227 r_angle_refined_deg 1.957 r_angle_other_deg 1.067 r_chiral_restr 0.163 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.283 r_dihedral_angle_4_deg 13.32 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_1_deg 6.227 r_angle_refined_deg 1.957 r_angle_other_deg 1.067 r_chiral_restr 0.163 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2421 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 70
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling