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Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, F43H, 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 19% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 20 mM MgCl2, 150 mM NaCl,
7.5 mg/ml ADH-A
Crystal Properties Matthews coefficient Solvent content 2.42 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.702 α = 90 b = 105.678 β = 91.51 c = 109.623 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 1.96 29.63 99.6 0.103 0.065 0.995 6.9 3.4 107618 24.2
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 1.96 1.99 93.7 0.764 0.489 0.574 1.5 3.3
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 1.96 29.63 102015 5190 99.89 0.177 0.17563 0.1845 0.20352 0.21 RANDOM 32.466
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] -0.71 0.21 1 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 17.395 r_dihedral_angle_3_deg 12.103 r_dihedral_angle_1_deg 5.74 r_long_range_B_other 5.687 r_long_range_B_refined 5.686 r_scangle_other 3.519 r_mcangle_it 2.74 r_mcangle_other 2.74 r_scbond_it 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 17.395 r_dihedral_angle_3_deg 12.103 r_dihedral_angle_1_deg 5.74 r_long_range_B_other 5.687 r_long_range_B_refined 5.686 r_scangle_other 3.519 r_mcangle_it 2.74 r_mcangle_other 2.74 r_scbond_it 2.263 r_scbond_other 2.263 r_mcbond_it 1.859 r_mcbond_other 1.859 r_angle_refined_deg 1.448 r_angle_other_deg 0.942 r_chiral_restr 0.077 r_bond_refined_d 0.01 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 9877 Nucleic Acid Atoms Solvent Atoms 1122 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing