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Bacteroides ovatus Xyloglucan PUL GH31 with bound 5FIdoF
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 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.906 α = 90 b = 108.448 β = 90 c = 144.853 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 6M 2014-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 48.28 99.7 0.089 0.999 12.2 7.8 193532
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 1.52 94 0.91 1.6 5.4
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 48.28 183662 9749 99.65 0.10927 0.10726 0.1072 0.14702 0.147 RANDOM 20.212
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] -0.09 -1.12 1.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.641 r_dihedral_angle_2_deg 35.143 r_dihedral_angle_4_deg 15.644 r_sphericity_bonded 11.644 r_dihedral_angle_3_deg 10.961 r_dihedral_angle_1_deg 6.353 r_long_range_B_refined 5.816 r_long_range_B_other 4.225 r_scangle_other 3.188 r_scbond_it 2.64
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.641 r_dihedral_angle_2_deg 35.143 r_dihedral_angle_4_deg 15.644 r_sphericity_bonded 11.644 r_dihedral_angle_3_deg 10.961 r_dihedral_angle_1_deg 6.353 r_long_range_B_refined 5.816 r_long_range_B_other 4.225 r_scangle_other 3.188 r_scbond_it 2.64 r_scbond_other 2.64 r_rigid_bond_restr 2.326 r_mcangle_other 1.983 r_mcangle_it 1.971 r_mcbond_it 1.61 r_mcbond_other 1.58 r_angle_refined_deg 1.529 r_angle_other_deg 0.966 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7658 Nucleic Acid Atoms Solvent Atoms 1466 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing