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Crystal structure of R. ruber ADH-A, mutant Y54G, L119Y
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 18% (w/v) PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mM 4'-Bromo-trifluoroacetophenone, 8 mg/ml ADH-A
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.555 α = 90 b = 105.969 β = 91.37 c = 108.076 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 1.83 29.56 98.8 0.077 0.072 0.995 7.3 3.4 127660 21.84
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 1.83 1.86 91.9 0.561 0.509 0.524 1.7 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 1.83 29.56 121109 6483 98.57 0.16942 0.16802 0.1774 0.19503 0.2032 RANDOM 28.541
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] -1.54 0.12 2.1 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.487 r_dihedral_angle_4_deg 14.658 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_1_deg 5.9 r_long_range_B_refined 4.82 r_long_range_B_other 4.779 r_scangle_other 3.282 r_mcangle_it 2.355 r_mcangle_other 2.354 r_scbond_it 2.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.487 r_dihedral_angle_4_deg 14.658 r_dihedral_angle_3_deg 12.471 r_dihedral_angle_1_deg 5.9 r_long_range_B_refined 4.82 r_long_range_B_other 4.779 r_scangle_other 3.282 r_mcangle_it 2.355 r_mcangle_other 2.354 r_scbond_it 2.161 r_scbond_other 2.161 r_mcbond_it 1.608 r_mcbond_other 1.606 r_angle_refined_deg 1.481 r_angle_other_deg 0.944 r_chiral_restr 0.078 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 9883 Nucleic Acid Atoms Solvent Atoms 1178 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing