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Horse liver alcohol dehydrogenase-NADH complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7 278 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA,
10 MG/ML PROTEIN, 1 MM NAD+, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL, MICRODIALYSIS, TEMPERATURE 278K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.158 α = 92.05 b = 50.911 β = 103.05 c = 92.66 γ = 109.6
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 4 2005-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9537 APS 19-ID
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 1.1 20 86.8 0.049 9.1 2.6 259214 8.8
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 1.1 1.2 71 0.535 2.3 1.86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4DWV 1.1 20 257968 1292 86.83 0.17678 0.17667 0.1829 0.19842 0.2023 RANDOM 19.04
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] 0.58 -0.16 0.13 0.86 0.21 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_sphericity_free 36.897 r_dihedral_angle_4_deg 13.637 r_dihedral_angle_3_deg 11.627 r_sphericity_bonded 9.791 r_dihedral_angle_1_deg 6.032 r_rigid_bond_restr 4.985 r_long_range_B_refined 4.45 r_long_range_B_other 3.377 r_scangle_other 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_sphericity_free 36.897 r_dihedral_angle_4_deg 13.637 r_dihedral_angle_3_deg 11.627 r_sphericity_bonded 9.791 r_dihedral_angle_1_deg 6.032 r_rigid_bond_restr 4.985 r_long_range_B_refined 4.45 r_long_range_B_other 3.377 r_scangle_other 2.912 r_scbond_it 2.626 r_scbond_other 2.625 r_angle_refined_deg 1.709 r_mcangle_other 1.695 r_mcangle_it 1.693 r_mcbond_it 1.48 r_mcbond_other 1.427 r_angle_other_deg 0.858 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing