7XFW

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.07 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
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.889α = 90
b = 101.508β = 90
c = 162.996γ = 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-10.97ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0746.3699.820.0410.998.136.9445175
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.1299.790.4330.8691.96

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-VALUE5DWF2.0746.35845174129799.8170.2020.19980.257636.53
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]
0.018-0.0210.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_3_deg15.165
r_dihedral_angle_4_deg14.04
r_dihedral_angle_1_deg7.39
r_lrange_it6.74
r_lrange_other6.738
r_scangle_it4.877
r_scangle_other4.877
r_mcangle_it3.878
r_mcangle_other3.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.479
r_dihedral_angle_3_deg15.165
r_dihedral_angle_4_deg14.04
r_dihedral_angle_1_deg7.39
r_lrange_it6.74
r_lrange_other6.738
r_scangle_it4.877
r_scangle_other4.877
r_mcangle_it3.878
r_mcangle_other3.877
r_scbond_it3.157
r_scbond_other3.156
r_mcbond_it2.71
r_mcbond_other2.709
r_angle_refined_deg1.498
r_angle_other_deg1.351
r_symmetry_xyhbond_nbd_refined0.23
r_symmetry_nbd_other0.2
r_nbd_refined0.199
r_xyhbond_nbd_refined0.189
r_nbd_other0.188
r_nbtor_refined0.162
r_symmetry_nbd_refined0.16
r_symmetry_xyhbond_nbd_other0.134
r_symmetry_nbtor_other0.084
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms467
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing