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Bacteroides ovatus Xyloglucan PUL GH3B with bound glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.2 M sodium acetate, 15-25% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.169 α = 90 b = 104.068 β = 90 c = 160.444 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 2012-12-16 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 2.3 47.57 99.9 0.151 0.995 11.4 8.1 72918
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 2.3 2.35 100 0.923 2.1 8.5
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 1ex1 2.3 47.57 69286 3561 99.85 0.17863 0.17697 0.1847 0.21086 0.217 RANDOM 35.059
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] 1.52 -0.12 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 18.979 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.641 r_long_range_B_other 6.307 r_long_range_B_refined 6.3 r_scangle_other 5.441 r_scbond_it 4.15 r_scbond_other 4.149 r_mcangle_it 3.684
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 18.979 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.641 r_long_range_B_other 6.307 r_long_range_B_refined 6.3 r_scangle_other 5.441 r_scbond_it 4.15 r_scbond_other 4.149 r_mcangle_it 3.684 r_mcangle_other 3.683 r_mcbond_it 2.811 r_mcbond_other 2.811 r_angle_refined_deg 1.412 r_angle_other_deg 1.036 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 11508 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing