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Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
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 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2.
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.17 α = 92.02 b = 51.59 β = 102.89 c = 92.77 γ = 110.04
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 210 2004-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 19.96 91.1 0.06 0.065 13.3 6.13 211946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 74.4 0.181 0.212 3.5
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 1.2 19.96 207414 2091 89.98 0.13518 0.13493 0.1349 0.1607 0.1607 RANDOM 17.445
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] 0.19 -0.33 0.06 0.53 0.11 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.392 r_dihedral_angle_4_deg 13.729 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_1_deg 6.595 r_rigid_bond_restr 4.988 r_scangle_other 3.215 r_scbond_it 3.139 r_scbond_other 3.139 r_long_range_B_refined 2.968 r_long_range_B_other 2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.392 r_dihedral_angle_4_deg 13.729 r_dihedral_angle_3_deg 12.183 r_dihedral_angle_1_deg 6.595 r_rigid_bond_restr 4.988 r_scangle_other 3.215 r_scbond_it 3.139 r_scbond_other 3.139 r_long_range_B_refined 2.968 r_long_range_B_other 2.85 r_angle_refined_deg 2.256 r_mcangle_it 1.719 r_mcangle_other 1.719 r_angle_other_deg 1.582 r_mcbond_it 1.551 r_mcbond_other 1.549 r_chiral_restr 0.139 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5568 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 126
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement d*TREK data reduction O model building