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Bacteroides ovatus Xyloglucan PUL GH31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XVG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.2 M potassium thiocyanate, 14-20% (w/v) PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.77 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.892 α = 90 b = 109.02 β = 90 c = 145.064 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 48.35 96.7 0.124 0.997 12.4 7.5 187821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 74.5 1.09 1 4.2
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 2xvg 1.5 48.35 178283 9444 96.53 0.16123 0.16004 0.1592 0.18354 0.1829 RANDOM 14.903
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] -0.52 -0.41 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 11.149 r_long_range_B_refined 6.788 r_long_range_B_other 6.788 r_dihedral_angle_1_deg 6.594 r_scangle_other 1.988 r_angle_refined_deg 1.41 r_mcangle_it 1.246 r_mcangle_other 1.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 11.149 r_long_range_B_refined 6.788 r_long_range_B_other 6.788 r_dihedral_angle_1_deg 6.594 r_scangle_other 1.988 r_angle_refined_deg 1.41 r_mcangle_it 1.246 r_mcangle_other 1.246 r_scbond_it 1.241 r_scbond_other 1.241 r_angle_other_deg 0.924 r_mcbond_it 0.768 r_mcbond_other 0.763 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 7631 Nucleic Acid Atoms Solvent Atoms 1644 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing