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X-ray structure of Lactobacillus kefir alcohol dehydrogenase (wild type)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293 50 mM Tris/HCl, 25 mM magnesium chloride, 5 % (w/v) PEG 3000, 10 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.87 α = 90 b = 79.97 β = 90 c = 114.59 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 2020-06-25 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 1.14 45.8 100 0.023 1 71.35 12.81 93534
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 1.14 1.21 99.8 0.083 0.998 26.89 11.99
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 4RF4 1.14 45.8 93486 4675 99.991 0.094 0.0931 0.0924 0.1072 0.106 8.254
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] 0.074 -0.093 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.685 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_3_deg 10.29 r_dihedral_angle_1_deg 6.66 r_lrange_it 2.902 r_lrange_other 2.32 r_rigid_bond_restr 2.005 r_angle_refined_deg 1.915 r_angle_other_deg 1.677 r_scangle_it 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.685 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_3_deg 10.29 r_dihedral_angle_1_deg 6.66 r_lrange_it 2.902 r_lrange_other 2.32 r_rigid_bond_restr 2.005 r_angle_refined_deg 1.915 r_angle_other_deg 1.677 r_scangle_it 1.453 r_scangle_other 1.453 r_scbond_it 1.159 r_scbond_other 1.159 r_mcangle_it 0.903 r_mcangle_other 0.903 r_mcbond_it 0.769 r_mcbond_other 0.769 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.232 r_nbd_other 0.218 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.171 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.11 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.013 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 1865 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing