3QJ1

Crystal structure of camel peptidoglycan recognition protein, PGRP-S with a trapped diethylene glycol in the ligand diffusion channel at 3.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OLK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82980.2M SODIUM POTASSIUM TARTRATE, 10% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4249.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.54α = 90
b = 100.596β = 90
c = 163.139γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2010-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.242.3597.80.12515122361223647.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.2692.80.3563.7

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 REPLACEMENTTHROUGHOUT3OLK3.242.35121381213861897.10.210.210.210.248RANDOM31.4
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]
-1.53-0.291.82
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_angle_deg1.7
c_improper_angle_d1.14
c_bond_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5348
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms23

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling