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Crystal structure of Haemophilus influenzae type b (Hib) DP2 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 6.5 293 0.01M Zinc sulfate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.665 α = 90 b = 131.588 β = 90 c = 145.096 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 EIGER2 X 16M 2019-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 2.29 51.5 99.7 0.162 0.995 7.3 7.8 26582 39.22
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 2.29 2.33 93.4 1.164 0.383 1.1 4.6
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 2.29 51.5 1.34 26531 1293 99.54 0.2277 0.2255 0.2276 0.2703 0.2696 46.09
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 9.0994 f_angle_d 0.6187 f_chiral_restr 0.0464 f_plane_restr 0.0044 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3307 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing