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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 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.11 α = 90 b = 81.17 β = 90 c = 132.36 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 IV++ 2006-10-31 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 2.4 19.87 95.5 0.059 12.3 4.16 17962
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) 2.4 2.49 98.2 0.213 4 3.95
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 2.4 19.87 17037 921 95.48 0.24673 0.24339 0.2364 0.30618 0.2954 RANDOM 35.033
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.551 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 15.982 r_dihedral_angle_1_deg 7.118 r_scangle_it 2.098 r_angle_refined_deg 1.456 r_scbond_it 1.407 r_mcangle_it 1.164 r_mcbond_it 0.678 r_symmetry_hbond_refined 0.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.551 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 15.982 r_dihedral_angle_1_deg 7.118 r_scangle_it 2.098 r_angle_refined_deg 1.456 r_scbond_it 1.407 r_mcangle_it 1.164 r_mcbond_it 0.678 r_symmetry_hbond_refined 0.404 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3387 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 19
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction