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X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q207D
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, 20mM HEPES/NaOH pH7.0, 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 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.82 α = 90 b = 80.52 β = 90 c = 115.1 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 2019-11-28 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 1.399 46.83 99.6 0.05 0.999 17.4 4.07 98425
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 1.4 1.49 98.6 0.174 0.9969 5.43 3.91
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 6h07 1.399 40.26 51330 2567 99.724 0.146 0.144 0.144 0.175 0.1748 16.542
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] -0.977 2.31 -1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.013 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 6.5 r_lrange_it 2.277 r_lrange_other 2.072 r_scangle_it 1.788 r_scangle_other 1.788 r_mcangle_it 1.478 r_mcangle_other 1.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 20.013 r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 6.5 r_lrange_it 2.277 r_lrange_other 2.072 r_scangle_it 1.788 r_scangle_other 1.788 r_mcangle_it 1.478 r_mcangle_other 1.478 r_angle_other_deg 1.401 r_scbond_it 1.378 r_scbond_other 1.378 r_angle_refined_deg 1.29 r_mcbond_it 1.223 r_mcbond_other 1.223 r_rigid_bond_restr 0.959 r_nbd_refined 0.208 r_nbd_other 0.206 r_symmetry_nbd_refined 0.197 r_symmetry_nbd_other 0.166 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.062 r_bond_refined_d 0.006 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 1870 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing