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Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 20 % PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris propane pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.538 α = 90 b = 95.455 β = 108.06 c = 79.016 γ = 90
Symmetry Space Group P 1 21 1
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 6M 2021-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.6 47.8 99.8 0.15 0.182 0.101 0.966 4.7 3.1 31116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 100 0.836 1.012 0.563 0.449 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.6 47.8 29547 1540 99.68 0.17998 0.17687 0.185 0.24143 0.2489 RANDOM 47.874
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] -3.64 0.7 2.33 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.891 r_dihedral_angle_4_deg 21.175 r_dihedral_angle_3_deg 16.274 r_long_range_B_other 10.086 r_long_range_B_refined 10.082 r_scangle_other 7.84 r_dihedral_angle_1_deg 6.931 r_mcangle_it 6.439 r_mcangle_other 6.439 r_scbond_it 5.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.891 r_dihedral_angle_4_deg 21.175 r_dihedral_angle_3_deg 16.274 r_long_range_B_other 10.086 r_long_range_B_refined 10.082 r_scangle_other 7.84 r_dihedral_angle_1_deg 6.931 r_mcangle_it 6.439 r_mcangle_other 6.439 r_scbond_it 5.318 r_scbond_other 5.318 r_mcbond_it 4.322 r_mcbond_other 4.322 r_angle_refined_deg 1.503 r_angle_other_deg 1.251 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7424 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing