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Crystal Structure of Alcohol Dehydrogenase from Anoxybacillus geothermalis D9
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 293.15 0.2M Magnesium chloride hexahydrate, 0.1M Bis Tris 5.5, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.607 α = 90 b = 130.769 β = 90.704 c = 134.918 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 293.15 PIXEL DECTRIS EIGER X 16M 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 48.97 99.81 0.082 0.983 7.9 2 79921
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 48.97 79628 4047 99.911 0.202 0.2003 0.2003 0.2408 0.2407 45.69
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] 0.064 -0.053 0.014 -0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.547 r_dihedral_angle_6_deg 15.321 r_lrange_other 14.588 r_lrange_it 14.587 r_scangle_it 11.866 r_scangle_other 11.865 r_dihedral_angle_2_deg 11.66 r_mcangle_it 9.005 r_mcangle_other 9.005 r_scbond_it 8.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.547 r_dihedral_angle_6_deg 15.321 r_lrange_other 14.588 r_lrange_it 14.587 r_scangle_it 11.866 r_scangle_other 11.865 r_dihedral_angle_2_deg 11.66 r_mcangle_it 9.005 r_mcangle_other 9.005 r_scbond_it 8.075 r_scbond_other 8.075 r_dihedral_angle_1_deg 7.71 r_mcbond_it 6.054 r_mcbond_other 6.049 r_angle_refined_deg 2.433 r_angle_other_deg 0.842 r_metal_ion_refined 0.583 r_xyhbond_nbd_refined 0.271 r_symmetry_nbd_refined 0.247 r_nbd_other 0.231 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_other 0.201 r_symmetry_nbd_other 0.163 r_nbtor_refined 0.16 r_chiral_restr 0.115 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_7 0.059 r_ncsr_local_group_18 0.058 r_ncsr_local_group_5 0.056 r_ncsr_local_group_27 0.056 r_ncsr_local_group_16 0.055 r_ncsr_local_group_2 0.054 r_ncsr_local_group_3 0.054 r_ncsr_local_group_13 0.054 r_ncsr_local_group_23 0.054 r_ncsr_local_group_1 0.053 r_ncsr_local_group_4 0.053 r_ncsr_local_group_10 0.053 r_ncsr_local_group_6 0.051 r_ncsr_local_group_17 0.051 r_ncsr_local_group_22 0.051 r_ncsr_local_group_26 0.051 r_ncsr_local_group_15 0.05 r_ncsr_local_group_8 0.049 r_ncsr_local_group_11 0.049 r_ncsr_local_group_12 0.048 r_ncsr_local_group_14 0.048 r_ncsr_local_group_9 0.047 r_ncsr_local_group_19 0.047 r_ncsr_local_group_21 0.046 r_ncsr_local_group_28 0.046 r_ncsr_local_group_20 0.045 r_ncsr_local_group_25 0.044 r_ncsr_local_group_24 0.041 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20256 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing