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F322L 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-2,4-PENTANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.26 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.37 α = 92.02 b = 51.28 β = 102.94 c = 92.5 γ = 110.01
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 2011-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.8865 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 1.26 20 82.8 0.077 9.4 3.34 166162 12.4
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 1.26 1.31 51.8 0.366 2.4 3.11
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 1.26 20 164103 1589 82.72 0.124 0.1238 0.1239 0.14416 0.1443 RANDOM 18.072
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] 0.28 -0.71 0.6 0.33 -0.41 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.592 r_sphericity_free 35.998 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_3_deg 11.548 r_sphericity_bonded 10.055 r_dihedral_angle_1_deg 6.157 r_long_range_B_refined 4.36 r_long_range_B_other 3.304 r_scangle_other 2.929 r_rigid_bond_restr 2.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.592 r_sphericity_free 35.998 r_dihedral_angle_4_deg 13.665 r_dihedral_angle_3_deg 11.548 r_sphericity_bonded 10.055 r_dihedral_angle_1_deg 6.157 r_long_range_B_refined 4.36 r_long_range_B_other 3.304 r_scangle_other 2.929 r_rigid_bond_restr 2.671 r_scbond_other 2.622 r_scbond_it 2.621 r_angle_refined_deg 1.872 r_mcangle_it 1.662 r_mcangle_other 1.662 r_mcbond_it 1.389 r_mcbond_other 1.389 r_angle_other_deg 1.056 r_chiral_restr 0.121 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5564 Nucleic Acid Atoms Solvent Atoms 972 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling REFMAC phasing