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Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2Q PDB ENTRY 1T2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2M potassium chloride, 0.05M HEPES, 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.464 α = 90 b = 74.464 β = 90 c = 149.893 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Vertical focusing mirror 2011-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9794 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 25 99.9 0.064 11 13.7 35967 2.2
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 1.95 2.02 100 0.556 12.8 3558
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 PDB ENTRY 1T2Q 1.95 24.45 35920 1793 99.81 0.2134 0.2117 0.2164 0.247 0.2498 RANDOM 63.074
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] 1.57 1.57 1.57 -5.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_4_deg 17.261 r_dihedral_angle_3_deg 16.123 r_dihedral_angle_1_deg 7.313 r_mcangle_it 2.483 r_mcbond_it 1.635 r_mcbond_other 1.633 r_angle_refined_deg 1.482 r_angle_other_deg 0.842 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.804 r_dihedral_angle_4_deg 17.261 r_dihedral_angle_3_deg 16.123 r_dihedral_angle_1_deg 7.313 r_mcangle_it 2.483 r_mcbond_it 1.635 r_mcbond_other 1.633 r_angle_refined_deg 1.482 r_angle_other_deg 0.842 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3368 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection