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Crystal structure of Haemophilus influenzae type b (Hib) DP3 oligosaccharide bound to Fab CA4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KYM experimental model PDB 6AZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.01M Nickel(II) chloride hexahydrate, 0.1M Tris pH 8.5, 20% w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 3.08 60.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.928 α = 90 b = 131.288 β = 90 c = 144.964 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 2020-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-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 2.74 65.64 96.8 0.18 0.94 5 3.5 15060 44.02
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 2.87 0.94 0.58 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.74 65.64 1.34 14988 757 95.52 0.2284 0.2259 0.2233 0.277 0.2716 43.62
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.5995 f_angle_d 0.6902 f_chiral_restr 0.0476 f_plane_restr 0.0048 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3282 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing