☰ Navigation Tabs
Crystal structure of R. ruber ADH-A, mutant Y54G, F43T, L119Y, F282W
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 510
100 mM Tris pH 8
4 mM NAD+
10 mM MgCl2
3 mg/ml ADHA mutant
Crystal Properties Matthews coefficient Solvent content 2.35 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.706 α = 90 b = 105.463 β = 91.4 c = 108.977 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 PILATUS3 6M 2017-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.74 29.5 94.1 0.06 0.07 0.036 0.998 11.5 3.5 143025 18.9
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 1.74 1.77 60.8 0.586 0.736 0.435 0.603 1.4 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3jv7 1.74 29.5 135478 7493 94.1 0.16388 0.16289 0.18132 0.1807 RANDOM 29.156
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] -1.23 0.34 1.12 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.777 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.655 r_dihedral_angle_1_deg 5.844 r_long_range_B_refined 5.338 r_long_range_B_other 5.031 r_angle_refined_deg 1.481 r_scangle_other 1.41 r_mcangle_it 1.128 r_mcangle_other 1.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.777 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.655 r_dihedral_angle_1_deg 5.844 r_long_range_B_refined 5.338 r_long_range_B_other 5.031 r_angle_refined_deg 1.481 r_scangle_other 1.41 r_mcangle_it 1.128 r_mcangle_other 1.128 r_angle_other_deg 0.945 r_scbond_it 0.86 r_scbond_other 0.86 r_mcbond_it 0.671 r_mcbond_other 0.67 r_chiral_restr 0.077 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 1381 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing