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Crystal structure of bacterial pectin methylesterase Pme8A 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 7.5 293 0.1 M Sodium HEPES 7.5, 20 % w/v PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.48 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.797 α = 90 b = 49.272 β = 101.03 c = 100.588 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 DECTRIS EIGER X 16M 2023-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95374 Australian Synchrotron MX2
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 48.76 97.3 0.105 0.114 0.044 0.997 8.8 6.8 48330
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 71 1.283 1.401 0.552 0.693 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 48.17 45937 2389 97.27 0.20245 0.2001 0.207 0.2495 0.2519 RANDOM 68.198
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] 0.14 -1.71 6.91 -5.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.536 r_dihedral_angle_2_deg 12.133 r_dihedral_angle_1_deg 7.583 r_long_range_B_refined 6.098 r_long_range_B_other 6.098 r_scangle_other 4.065 r_mcangle_it 3.394 r_mcangle_other 3.394 r_scbond_it 2.517 r_scbond_other 2.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.536 r_dihedral_angle_2_deg 12.133 r_dihedral_angle_1_deg 7.583 r_long_range_B_refined 6.098 r_long_range_B_other 6.098 r_scangle_other 4.065 r_mcangle_it 3.394 r_mcangle_other 3.394 r_scbond_it 2.517 r_scbond_other 2.516 r_mcbond_it 2.138 r_mcbond_other 2.137 r_angle_refined_deg 1.392 r_angle_other_deg 0.455 r_chiral_restr 0.062 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 7872 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing