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X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q126K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 Protein solution (10 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (1 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME)
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.77 α = 90 b = 84.23 β = 90 c = 113.56 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 2019-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.966000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.21 46.466 98.9 0.999 10.36 5.07 81466
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.28 97.7 0.638 4.4
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 6h07 1.21 35.98 77296 4069 98.99 0.1498 0.1486 0.1624 0.1723 0.1873 RANDOM 16.963
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] 0.94 -1.44 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 21.179 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 7.029 r_rigid_bond_restr 1.931 r_angle_refined_deg 1.585 r_angle_other_deg 1.541 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 21.179 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 7.029 r_rigid_bond_restr 1.931 r_angle_refined_deg 1.585 r_angle_other_deg 1.541 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1871 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing