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Crystal structure of R. ruber ADH-A, mutant F43H, Y54L
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 8 293 15% Polyacrylic acid 5100
0.1 M Tris pH 8
4 mM NAD+
20 mM MgCl2
7.5 mg/ml ADHA mutant
Crystal Properties Matthews coefficient Solvent content 2.32 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.497 α = 90 b = 105.572 β = 91.51 c = 108.658 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) Rrim I (All) 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 1.71 29.5 98.3 0.088 0.104 0.056 0.989 6.3 3.2 156099 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 74.2 0.657 0.856 0.542 0.503 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 3jv7 1.71 29.5 147820 7867 98.13 0.16246 0.16139 0.1715 0.18273 0.1907 RANDOM 28.716
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] -0.42 0.38 0.31 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.007 r_dihedral_angle_4_deg 15.87 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 5.788 r_long_range_B_refined 5.207 r_long_range_B_other 4.781 r_scangle_other 1.518 r_angle_refined_deg 1.465 r_mcangle_it 1.284 r_mcangle_other 1.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.007 r_dihedral_angle_4_deg 15.87 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 5.788 r_long_range_B_refined 5.207 r_long_range_B_other 4.781 r_scangle_other 1.518 r_angle_refined_deg 1.465 r_mcangle_it 1.284 r_mcangle_other 1.284 r_angle_other_deg 0.938 r_scbond_it 0.927 r_scbond_other 0.927 r_mcbond_it 0.763 r_mcbond_other 0.763 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 9893 Nucleic Acid Atoms Solvent Atoms 1444 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing