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GH2 beta-galacturonate AqGalA in complex with galacturonide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM MOPSO buffer (pH6.5), 12.5% PEG4000, and 20% 1,2,6-hexanetriol
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.413 α = 90 b = 154.006 β = 109.78 c = 115.925 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 100 PIXEL DECTRIS PILATUS3 R 200K-A 2021-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54056
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 2.4 19.95 99.7 0.138 0.154 0.065 0.972 7.2 5.4 107088
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 2.4 2.44 99.8 0.455 0.546 0.298 0.804 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6D1N 2.4 19.95 100697 5309 98.74 0.2025 0.1996 0.2047 0.2573 0.2577 RANDOM 21.632
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] -0.15 0.24 1.74 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_4_deg 15.603 r_dihedral_angle_1_deg 7.984 r_angle_refined_deg 1.529 r_angle_other_deg 1.226 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_4_deg 15.603 r_dihedral_angle_1_deg 7.984 r_angle_refined_deg 1.529 r_angle_other_deg 1.226 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19388 Nucleic Acid Atoms Solvent Atoms 1266 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing