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Type I PQQ-dependent alcohol dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG400, Imidazole, PEGMME5000
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.85 α = 90 b = 94.301 β = 108.2 c = 56.587 γ = 90
Symmetry Space Group C 1 2 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 Bruker PHOTON II 2024-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 44.53 99.8 0.934 9.1 2.6 31023
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 2.1 2.16 0.45
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 2.1 44.52 29502 1494 99.63 0.17257 0.17033 0.1809 0.21714 0.2288 RANDOM 15.026
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] -0.42 -0.45 1.01 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 17.735 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 7.158 r_long_range_B_refined 3.596 r_long_range_B_other 3.235 r_scangle_other 1.508 r_angle_refined_deg 1.364 r_mcangle_it 1.278 r_mcangle_other 1.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.675 r_dihedral_angle_4_deg 17.735 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 7.158 r_long_range_B_refined 3.596 r_long_range_B_other 3.235 r_scangle_other 1.508 r_angle_refined_deg 1.364 r_mcangle_it 1.278 r_mcangle_other 1.278 r_scbond_it 0.891 r_scbond_other 0.884 r_angle_other_deg 0.766 r_mcbond_it 0.745 r_mcbond_other 0.742 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4231 Nucleic Acid Atoms Solvent Atoms 430 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement APEX data reduction APEX data scaling PHASER phasing