☰ Navigation Tabs
Crystal structure of group B Streptococcus type III DP2 oligosaccharide bound to Fab NVS-1-19-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 0.1 M Cadmium chloride hemi (pentahydrate), 30% (v/v) PEG 400, 0.1 M sodium acetate, pH 4.6 (Structure Screen 1 & 2 HT-96; Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.341 α = 90 b = 142.231 β = 90 c = 144.732 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 2M 2016-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.74 49.02 99 0.08093 0.998 12.12 4.5 36702 67.72
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 2.74 2.838 96 0.7761 0.649 1.45 4.1
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 4JO1 2.74 49.02 34868 1834 99.18 0.23784 0.23552 0.2365 0.28218 0.2816 RANDOM 69.419
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] -0.23 -1.11 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.765 r_dihedral_angle_3_deg 16.777 r_dihedral_angle_4_deg 14.669 r_dihedral_angle_1_deg 9.598 r_long_range_B_refined 4.703 r_long_range_B_other 4.686 r_mcangle_it 2.746 r_mcangle_other 2.746 r_scangle_other 2.475 r_angle_refined_deg 1.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.765 r_dihedral_angle_3_deg 16.777 r_dihedral_angle_4_deg 14.669 r_dihedral_angle_1_deg 9.598 r_long_range_B_refined 4.703 r_long_range_B_other 4.686 r_mcangle_it 2.746 r_mcangle_other 2.746 r_scangle_other 2.475 r_angle_refined_deg 1.564 r_mcbond_it 1.538 r_mcbond_other 1.538 r_scbond_it 1.464 r_scbond_other 1.464 r_angle_other_deg 0.928 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 6480 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 316
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing