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X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F
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 7 293 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 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.76 α = 90 b = 81.09 β = 90 c = 113.13 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 16M 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000089622351307 SLS X06SA
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 1.408 46.39 98 0.999 15.73 13.41 97917
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 1.408 1.44 94.5 0.606
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 1.41 46.39 93011 4897 97.92 0.1274 0.1256 0.1311 0.1624 0.1671 RANDOM 16.451
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] 0.26 0.87 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.597 r_dihedral_angle_4_deg 23.4 r_dihedral_angle_3_deg 11.541 r_dihedral_angle_1_deg 6.807 r_angle_other_deg 1.477 r_angle_refined_deg 1.382 r_rigid_bond_restr 1.218 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.597 r_dihedral_angle_4_deg 23.4 r_dihedral_angle_3_deg 11.541 r_dihedral_angle_1_deg 6.807 r_angle_other_deg 1.477 r_angle_refined_deg 1.382 r_rigid_bond_restr 1.218 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3748 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing