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SusD protein from human gut uncultured Bacteroides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other from Morda server
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 1.7M Na3Citrate, 15% Glycerol, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 5.31 76.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.086 α = 90 b = 179.086 β = 90 c = 182.229 γ = 90
Symmetry Space Group I 41 2 2
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 2019-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
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 2.65 127.73 100 0.062 0.99 8.4 7.1 43113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.79 0.736 0.86
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 from Morda server 2.65 127.73 41009 2089 99.91 0.18623 0.18503 0.1897 0.21178 0.2145 RANDOM 85.816
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] -4.28 -4.28 8.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_1_deg 5.618 r_long_range_B_refined 4.709 r_long_range_B_other 4.709 r_mcangle_it 2.102 r_mcangle_other 2.102 r_scangle_other 1.847 r_mcbond_it 1.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 14.485 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_1_deg 5.618 r_long_range_B_refined 4.709 r_long_range_B_other 4.709 r_mcangle_it 2.102 r_mcangle_other 2.102 r_scangle_other 1.847 r_mcbond_it 1.217 r_mcbond_other 1.217 r_angle_refined_deg 1.113 r_scbond_it 1.076 r_scbond_other 1.074 r_angle_other_deg 0.769 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 4849 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing