7XFX

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DWF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529810% PEG 3350 0.2M Sodium potassium tartrate 20% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4249.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.661α = 90
b = 101.653β = 90
c = 163.328γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2018-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.2878.0480.680.1160.050.99810.86.827481
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.321000.8280.350.9072.56.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5DWF2.2877.92127481134180.6790.1910.18770.25526.517
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]
-0.0940.0460.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.672
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg15.572
r_dihedral_angle_1_deg7.548
r_lrange_it5.732
r_lrange_other5.732
r_scangle_it3.473
r_scangle_other3.472
r_mcangle_it3
r_mcangle_other2.999
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.672
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg15.572
r_dihedral_angle_1_deg7.548
r_lrange_it5.732
r_lrange_other5.732
r_scangle_it3.473
r_scangle_other3.472
r_mcangle_it3
r_mcangle_other2.999
r_scbond_it2.104
r_scbond_other2.104
r_mcbond_other1.775
r_mcbond_it1.774
r_angle_refined_deg1.432
r_angle_other_deg1.269
r_nbd_refined0.194
r_symmetry_nbd_other0.194
r_nbd_other0.177
r_xyhbond_nbd_refined0.173
r_nbtor_refined0.159
r_symmetry_nbd_refined0.147
r_symmetry_xyhbond_nbd_refined0.147
r_symmetry_xyhbond_nbd_other0.092
r_symmetry_nbtor_other0.08
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5203
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing