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Crystal structure of bacterial pectin methylesterase PmeC2 from rumen Butyrivibrio
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 8.5 298 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 20 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.57 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.638 α = 98.36 b = 76.282 β = 104.16 c = 96.779 γ = 90.05
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 EIGER2 S 9M 2023-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95372 Australian Synchrotron MX1
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 2.3 47.2 95.1 0.148 0.173 0.089 0.994 5.4 3.7 56000
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 2.3 2.37 92.3 1.404 1.639 0.842 0.349 3.6
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 2.3 47.17 53208 2790 95.11 0.20625 0.20448 0.2091 0.24013 0.2401 RANDOM 42.514
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] -2.12 -0.31 -0.54 1.18 -0.28 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.824 r_dihedral_angle_1_deg 7.623 r_dihedral_angle_2_deg 6.79 r_long_range_B_refined 5.043 r_long_range_B_other 5.028 r_scangle_other 2.763 r_mcangle_it 2.603 r_mcangle_other 2.602 r_scbond_it 1.652 r_scbond_other 1.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.824 r_dihedral_angle_1_deg 7.623 r_dihedral_angle_2_deg 6.79 r_long_range_B_refined 5.043 r_long_range_B_other 5.028 r_scangle_other 2.763 r_mcangle_it 2.603 r_mcangle_other 2.602 r_scbond_it 1.652 r_scbond_other 1.652 r_mcbond_it 1.561 r_mcbond_other 1.56 r_angle_refined_deg 1.298 r_angle_other_deg 0.454 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9128 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing