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Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q7B Swissmodel based on pdb entries 1Q7B and 1EDO experimental model PDB 1EDO Swissmodel based on pdb entries 1Q7B and 1EDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 200 mM sodium fluoride, 20% PEG3350, 10% ethylene glycol plus 5mM NAD+, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.839 α = 90 b = 62.429 β = 99.22 c = 102.439 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 MARMOSAIC 225 mm CCD 2007-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00234 SLS X10SA
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 50 99.9 0.117 3.5 54998
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 2.07 100 0.759 3.3
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 Swissmodel based on pdb entries 1Q7B and 1EDO 2 46 54998 54998 2937 99.6 0.18616 0.18616 0.18394 0.1908 0.22667 0.2351 RANDOM 31.061
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] -1.1 -0.05 0.86 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 14.421 r_dihedral_angle_3_deg 12.584 r_dihedral_angle_1_deg 5.641 r_scangle_it 3.062 r_scbond_it 2.025 r_angle_refined_deg 1.354 r_mcangle_it 1.228 r_angle_other_deg 0.896 r_mcbond_it 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_4_deg 14.421 r_dihedral_angle_3_deg 12.584 r_dihedral_angle_1_deg 5.641 r_scangle_it 3.062 r_scbond_it 2.025 r_angle_refined_deg 1.354 r_mcangle_it 1.228 r_angle_other_deg 0.896 r_mcbond_it 0.802 r_symmetry_hbond_refined 0.433 r_symmetry_vdw_other 0.273 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.203 r_mcbond_other 0.194 r_nbd_other 0.183 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.087 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6605 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing