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Structure of a thermostable Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1M Bis-Tris pH7.2
36% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.59 52.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.867 α = 90 b = 102.867 β = 90 c = 65.908 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD BRUKER SMART 6000 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 24.71 93.1 0.058 2.79 5 18868 25.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 10 0.058
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5Z2X 2.20042955034 24.7078541962 1.33750969307 18868 953 93.0512403215 0.188526221083 0.186378116785 0.1919 0.230901236109 0.2319 31.9609593147
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.40022666589 f_angle_d 0.749103387183 f_chiral_restr 0.0460294630405 f_plane_restr 0.00477867510687 f_bond_d 0.00422387371839
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2742 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing