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I220L horse liver alcohol dehydrogenase complexed with NAD and 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 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+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-,4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.27 α = 91.75 b = 51.53 β = 103.12 c = 92.44 γ = 109.34
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 NOIR-1 2009-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.80 ALS 4.2.2
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 1.4 20 91 0.051 11.3 3.64 132451
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 1.4 1.436 86.77 0.373 2.3 3.61
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 1.4 20 132451 1340 91.04 0.13246 0.13194 0.1404 0.18411 0.1854 RANDOM 23.44
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] 0.14 0.63 -0.14 1.57 -0.08 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_sphericity_free 30.412 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_3_deg 12.072 r_sphericity_bonded 10.302 r_dihedral_angle_1_deg 6.317 r_long_range_B_refined 4.378 r_scangle_other 3.899 r_long_range_B_other 3.789 r_rigid_bond_restr 3.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_sphericity_free 30.412 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_3_deg 12.072 r_sphericity_bonded 10.302 r_dihedral_angle_1_deg 6.317 r_long_range_B_refined 4.378 r_scangle_other 3.899 r_long_range_B_other 3.789 r_rigid_bond_restr 3.726 r_scbond_other 3.581 r_scbond_it 3.575 r_mcangle_it 2.356 r_mcangle_other 2.356 r_mcbond_it 2.127 r_mcbond_other 2.127 r_angle_refined_deg 1.702 r_angle_other_deg 0.877 r_chiral_restr 0.101 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 864 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling O model building REFMAC phasing