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The structure of wild-type human HADH2 (17beta-hydroxysteroid dehydrogenase type 10) bound to NAD+ at 1.2 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U7T pdb entry 1U7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 25.5% PEG 3350, 15% glycerol, 0.17 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.037 α = 90 b = 117.037 β = 90 c = 69.087 γ = 120
Symmetry Space Group P 32 2 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 MARRESEARCH 2006-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.2 50 99.5 0.092 8.1 3.6 168585 168585 11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.26 99.2 1.9 2.9 24386
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 1U7T 1.2 50 166548 166548 1996 99.49 0.123 0.123 0.12264 0.1341 0.15395 0.1641 RANDOM 11.171
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] -0.45 -0.22 -0.45 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_sphericity_free 20.149 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_3_deg 11.222 r_scangle_it 8.854 r_scbond_it 7.416 r_sphericity_bonded 7.413 r_dihedral_angle_1_deg 5.857 r_mcangle_it 5.149 r_mcbond_it 4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.888 r_sphericity_free 20.149 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_3_deg 11.222 r_scangle_it 8.854 r_scbond_it 7.416 r_sphericity_bonded 7.413 r_dihedral_angle_1_deg 5.857 r_mcangle_it 5.149 r_mcbond_it 4.51 r_rigid_bond_restr 3.737 r_mcbond_other 2.796 r_angle_refined_deg 1.55 r_angle_other_deg 0.961 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.224 r_symmetry_vdw_other 0.215 r_nbd_other 0.194 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.091 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3582 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing