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Bacteroides ovatus Xyloglucan PUL GH43B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 0.2 M sodium acetate pH 5, 20-30% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.46 α = 90 b = 71.4 β = 94.78 c = 160.3 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 PILATUS3 6M 2013-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.980 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.28 52.19 99.6 0.092 11.1 4.1 46976
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 2.28 2.34 99.5 0.624 2.3 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 1yrz 2.28 52.19 44617 2358 99.54 0.19513 0.19222 0.1975 0.25023 0.2538 RANDOM 34.601
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] 1.38 0.83 -3.41 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.905 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 13.198 r_dihedral_angle_1_deg 6.77 r_long_range_B_other 6.621 r_long_range_B_refined 6.62 r_scangle_other 5.066 r_mcangle_it 4.474 r_mcangle_other 4.473 r_scbond_it 3.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.905 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 13.198 r_dihedral_angle_1_deg 6.77 r_long_range_B_other 6.621 r_long_range_B_refined 6.62 r_scangle_other 5.066 r_mcangle_it 4.474 r_mcangle_other 4.473 r_scbond_it 3.593 r_scbond_other 3.592 r_mcbond_it 3.171 r_mcbond_other 3.168 r_angle_refined_deg 1.324 r_angle_other_deg 0.911 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 7723 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing