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Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HET PDB ENTRY 1HET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 DIALYSIS 30 MM TRIS/HCL PH 8.2 25 % MPD
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.186 α = 77.12 b = 43.798 β = 87.44 c = 92.516 γ = 108.89
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 25 94.1 0.05 17.8 2.6 212570
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 1.2 1.23 89.1 0.22 2.8 2
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 PDB ENTRY 1HET 1.2 19.83 209920 2129 94 0.115 0.114 0.1312 0.142 0.151 RANDOM 13.31
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] 0.27 -0.04 -0.04 0.01 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.811 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_4_deg 12.407 r_dihedral_angle_1_deg 6.219 r_scangle_it 4.144 r_scbond_it 3.289 r_mcangle_it 2.36 r_mcbond_it 1.983 r_angle_refined_deg 1.929 r_angle_other_deg 1.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.811 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_4_deg 12.407 r_dihedral_angle_1_deg 6.219 r_scangle_it 4.144 r_scbond_it 3.289 r_mcangle_it 2.36 r_mcbond_it 1.983 r_angle_refined_deg 1.929 r_angle_other_deg 1.094 r_nbd_refined 0.267 r_symmetry_vdw_other 0.234 r_symmetry_hbond_refined 0.228 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.195 r_nbtor_refined 0.185 r_symmetry_vdw_refined 0.174 r_nbtor_other 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5570 Nucleic Acid Atoms Solvent Atoms 1236 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling