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Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43S, H39Y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 15% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 1 mM MgCl2, 7.5 mg/ml ADH-A
Crystal Properties Matthews coefficient Solvent content 2.31 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.842 α = 90 b = 105.293 β = 91.36 c = 109.287 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.64 29.53 97.2 0.079 0.05 0.996 7.1 3.3 177639 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.66 68.7 0.539 0.393 0.66 1.2 2.3
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 3jv7 1.64 29.5 168316 8693 97.26 0.16881 0.16793 0.1795 0.18556 0.196 RANDOM 26.418
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] 0.17 0.35 0.68 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.643 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_1_deg 5.745 r_long_range_B_other 5.356 r_long_range_B_refined 5.355 r_angle_refined_deg 1.476 r_scangle_other 1.421 r_mcangle_it 0.984 r_mcangle_other 0.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.643 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_1_deg 5.745 r_long_range_B_other 5.356 r_long_range_B_refined 5.355 r_angle_refined_deg 1.476 r_scangle_other 1.421 r_mcangle_it 0.984 r_mcangle_other 0.984 r_angle_other_deg 0.94 r_scbond_it 0.893 r_scbond_other 0.893 r_mcbond_it 0.594 r_mcbond_other 0.594 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9859 Nucleic Acid Atoms Solvent Atoms 1612 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing