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co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.85 α = 90 b = 81.29 β = 90 c = 132.34 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 IMAGE PLATE RIGAKU RAXIS 2007-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.8 19.97 94.5 0.073 9 3.49 44150
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) 1.8 1.86 99.5 0.228 4 3.73 4550
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 MOLECULAR REPLACEMENT THROUGHOUT 1.85 20 40510 2071 94.01 0.226 0.224 0.2217 0.273 0.2702 RANDOM 22.304
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 -0.8 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.15 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_1_deg 7.12 r_scangle_it 3.656 r_scbond_it 2.629 r_angle_refined_deg 1.723 r_mcangle_it 1.571 r_mcbond_it 1.002 r_symmetry_metal_ion_refined 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.15 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_1_deg 7.12 r_scangle_it 3.656 r_scbond_it 2.629 r_angle_refined_deg 1.723 r_mcangle_it 1.571 r_mcbond_it 1.002 r_symmetry_metal_ion_refined 0.428 r_nbtor_refined 0.302 r_xyhbond_nbd_refined 0.284 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.123 r_metal_ion_refined 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3315 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 36
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction