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Crystal structure of S25-2 Fab in complex with Kdo analogues
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 300 PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.89 α = 90 b = 81.66 β = 90 c = 131.55 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.6 19.92 95.7 0.044 11.8 3.03 63260
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) 1.6 1.66 99.1 0.267 3.6 3.1 6423
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.6 20 63237 3212 95.67 0.232 0.231 0.2234 0.253 0.249 RANDOM 19.985
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] 0.64 -0.38 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_4_deg 17.935 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.965 r_scbond_it 2.137 r_angle_refined_deg 1.406 r_mcangle_it 1.372 r_mcbond_it 0.846 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_4_deg 17.935 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.965 r_scbond_it 2.137 r_angle_refined_deg 1.406 r_mcangle_it 1.372 r_mcbond_it 0.846 r_nbtor_refined 0.301 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.096 r_metal_ion_refined 0.031 r_symmetry_metal_ion_refined 0.028 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3335 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 51
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction