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Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S2J pdb entries 1S2J and 1Z6I experimental model PDB 1Z6I pdb entries 1S2J and 1Z6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.2 298 20% polyethylene glycol 1500, 5% ethylene glycol, and 100 mM phosphate-citrate, pH 4.2, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.123 α = 90 b = 79.695 β = 90 c = 114.389 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 110 CCD CUSTOM-MADE 2005-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97950 APS 19-ID
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 2.05 50 98 0.088 5.9 24185 23701 -3 -3
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 2.05 2.09 90.2 0.497 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 1S2J and 1Z6I 2.1 30 22645 21203 1148 98.55 0.16872 0.16872 0.1663 0.21378 0.2594 RANDOM 19.17
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] 1.01 -2.05 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.928 r_dihedral_angle_4_deg 18.863 r_dihedral_angle_3_deg 13.694 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.226 r_scbond_it 1.417 r_angle_refined_deg 1.329 r_angle_other_deg 0.798 r_mcangle_it 0.674 r_mcbond_it 0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.928 r_dihedral_angle_4_deg 18.863 r_dihedral_angle_3_deg 13.694 r_dihedral_angle_1_deg 5.917 r_scangle_it 2.226 r_scbond_it 1.417 r_angle_refined_deg 1.329 r_angle_other_deg 0.798 r_mcangle_it 0.674 r_mcbond_it 0.524 r_symmetry_vdw_other 0.251 r_nbd_refined 0.193 r_nbd_other 0.181 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.16 r_mcbond_other 0.111 r_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2653 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing