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Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0% PEG 500 MME, 10% PEG20K, 0.1M Sodium HEPES/MOPS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.65 53.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.313 α = 90 b = 85.566 β = 98.94 c = 112.628 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 PILATUS 6M-F 2018-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 2.1 104.25 99.9 0.135 0.159 0.083 0.988 5.4 3.5 115358
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 2.1 2.14 100 0.858 1.016 0.538 0.342 3.5
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 4D6C 2.1 104.03 109735 5601 99.89 0.1765 0.1749 0.1879 0.2063 0.2178 RANDOM 38.933
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] -0.65 0.18 -1.41 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 13.256 r_dihedral_angle_1_deg 6.999 r_angle_refined_deg 1.313 r_angle_other_deg 1.21 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 13.256 r_dihedral_angle_1_deg 6.999 r_angle_refined_deg 1.313 r_angle_other_deg 1.21 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13381 Nucleic Acid Atoms Solvent Atoms 1128 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing