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Crystal structure of R. ruber ADH-A, mutant F43H
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 17% Polyacrylic acid 5100
0.1 M Tris pH 8
4 mM NAD+
20 mM MgCl2
100 mM phenylethandiol
7.5 mg/ml ADHA-mutant
Crystal Properties Matthews coefficient Solvent content 2.64 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.647 α = 90 b = 103.162 β = 90.74 c = 111.187 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 2.49 29.33 98.8 0.08 0.096 0.053 0.995 7.9 3.2 51089 78.9
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 2.49 2.57 87 0.607 0.748 0.431 0.709 2.8
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 2.5 29.3 47961 2592 98.38 0.22295 0.22123 0.2208 0.25257 0.2454 RANDOM 77.513
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] -3.85 1.8 4.22 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 13.884 r_dihedral_angle_1_deg 5.831 r_long_range_B_refined 3.667 r_long_range_B_other 3.661 r_mcangle_it 2.274 r_mcangle_other 2.274 r_scangle_other 2.067 r_angle_refined_deg 1.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 13.884 r_dihedral_angle_1_deg 5.831 r_long_range_B_refined 3.667 r_long_range_B_other 3.661 r_mcangle_it 2.274 r_mcangle_other 2.274 r_scangle_other 2.067 r_angle_refined_deg 1.412 r_mcbond_it 1.363 r_mcbond_other 1.363 r_scbond_it 1.241 r_scbond_other 1.241 r_angle_other_deg 0.925 r_chiral_restr 0.069 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 9916 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing