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1,2-propanediol dehydratase with 0.1 % 1,2-propanediol additive
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 8.5 293 0.6 M ammonium acetate, 4% PEG
4000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.89 α = 90 b = 199.973 β = 106.323 c = 118.377 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 90 PIXEL DECTRIS EIGER2 XE 16M 2025-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 2.8 98.78 97.3 0.858 1.03 0.561 0.3 4.3 6.3 86164 35.67
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 2.8 2.85 92.9 5.835 11.338 4.087 0.192 1.2 5.4
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 2.8 98.7 85965 4009 97.074 0.265 0.2626 0.2581 0.3178 0.3131 26.739
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] 1.912 1.34 -2.38 -0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.623 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 15.81 r_dihedral_angle_1_deg 7.578 r_lrange_it 3.642 r_lrange_other 3.642 r_scangle_it 2.779 r_scangle_other 2.779 r_mcangle_it 2.438 r_mcangle_other 2.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.623 r_dihedral_angle_4_deg 19.099 r_dihedral_angle_3_deg 15.81 r_dihedral_angle_1_deg 7.578 r_lrange_it 3.642 r_lrange_other 3.642 r_scangle_it 2.779 r_scangle_other 2.779 r_mcangle_it 2.438 r_mcangle_other 2.438 r_scbond_it 1.886 r_scbond_other 1.886 r_mcbond_it 1.571 r_mcbond_other 1.57 r_angle_other_deg 1.51 r_angle_refined_deg 1.328 r_symmetry_xyhbond_nbd_refined 0.33 r_nbd_other 0.325 r_symmetry_nbd_refined 0.282 r_symmetry_nbd_other 0.219 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_bond_other_d 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25001 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing