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X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant T102E
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 VAPOR DIFFUSION, SITTING DROP 7 293 Protein solution ( 10 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (100 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME)
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.62 α = 90 b = 81.15 β = 90 c = 115.56 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 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 1.000 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 1.44 47.068 99.7 0.109 0.999 16.16 12.9 94960
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 1.44 1.47 99.9 0.683 2.06 13
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 1.44 47.068 94959 4748 99.633 0.132 0.1297 0.1297 0.1684 0.1685 16.333
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] -1.55 1.027 0.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.009 r_dihedral_angle_4_deg 19.928 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_1_deg 6.474 r_lrange_it 3.561 r_lrange_other 2.772 r_scangle_it 1.697 r_scangle_other 1.697 r_angle_other_deg 1.411 r_scbond_other 1.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.009 r_dihedral_angle_4_deg 19.928 r_dihedral_angle_3_deg 11.379 r_dihedral_angle_1_deg 6.474 r_lrange_it 3.561 r_lrange_other 2.772 r_scangle_it 1.697 r_scangle_other 1.697 r_angle_other_deg 1.411 r_scbond_other 1.385 r_scbond_it 1.384 r_mcangle_it 1.363 r_mcangle_other 1.362 r_angle_refined_deg 1.28 r_mcbond_it 1.043 r_mcbond_other 1.043 r_rigid_bond_restr 0.769 r_nbd_refined 0.227 r_nbd_other 0.184 r_symmetry_nbd_other 0.174 r_symmetry_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.16 r_nbtor_refined 0.156 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3746 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASES phasing