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X-ray structure of Lactobacillus kefir alcohol dehydrogenase mutant Q126K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293 50 mM Tris/HCl, 25 mM magnesium chloride, 5 % (w/v) PEG 550, 10 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.84 α = 90 b = 80.04 β = 90 c = 114.93 γ = 90
Symmetry Space Group I 2 2 2
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 2M-F 2020-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.25 50 99.2 0.033 1 49.61 11.62 71194
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.32 95.3 0.109 0.993 14.32
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7P36 1.25 45.796 70930 1419 99.347 0.101 0.1005 0.0996 0.1175 0.1176 9.684
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] -0.207 0.792 -0.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.007 r_dihedral_angle_4_deg 14.938 r_dihedral_angle_3_deg 11.72 r_dihedral_angle_1_deg 6.508 r_lrange_it 2.336 r_lrange_other 1.906 r_rigid_bond_restr 1.872 r_angle_refined_deg 1.778 r_scangle_it 1.666 r_scangle_other 1.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.007 r_dihedral_angle_4_deg 14.938 r_dihedral_angle_3_deg 11.72 r_dihedral_angle_1_deg 6.508 r_lrange_it 2.336 r_lrange_other 1.906 r_rigid_bond_restr 1.872 r_angle_refined_deg 1.778 r_scangle_it 1.666 r_scangle_other 1.665 r_angle_other_deg 1.664 r_scbond_it 1.347 r_scbond_other 1.347 r_mcangle_it 1.1 r_mcangle_other 1.099 r_mcbond_it 0.866 r_mcbond_other 0.866 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.19 r_nbd_other 0.181 r_nbtor_refined 0.177 r_symmetry_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing