2F2L

Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S2Jpdb entries 1S2J and 1Z6I
experimental modelPDB 1Z6Ipdb entries 1S2J and 1Z6I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.229820% polyethylene glycol 1500, 5% ethylene glycol, and 100 mM phosphate-citrate, pH 4.2, EVAPORATION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.123α = 90
b = 79.695β = 90
c = 114.389γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDCUSTOM-MADE2005-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97950APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0550980.0885.92418523701-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.0990.20.4972

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entries 1S2J and 1Z6I2.1302264521203114898.550.168720.168720.16630.21378RANDOM19.17
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]
1.01-2.051.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.928
r_dihedral_angle_4_deg18.863
r_dihedral_angle_3_deg13.694
r_dihedral_angle_1_deg5.917
r_scangle_it2.226
r_scbond_it1.417
r_angle_refined_deg1.329
r_angle_other_deg0.798
r_mcangle_it0.674
r_mcbond_it0.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.928
r_dihedral_angle_4_deg18.863
r_dihedral_angle_3_deg13.694
r_dihedral_angle_1_deg5.917
r_scangle_it2.226
r_scbond_it1.417
r_angle_refined_deg1.329
r_angle_other_deg0.798
r_mcangle_it0.674
r_mcbond_it0.524
r_symmetry_vdw_other0.251
r_nbd_refined0.193
r_nbd_other0.181
r_nbtor_refined0.177
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.16
r_mcbond_other0.111
r_nbtor_other0.084
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2653
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing