3NG4

Ternary complex of peptidoglycan recognition protein (PGRP-S) with Maltose and N-Acetylglucosamine at 1.7 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C2X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22980.2M NAKTARTRATE, 10% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.128α = 90
b = 100.784β = 90
c = 161.85γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2009-07-24MSINGLE 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
11.785.5990.04732.78773377733720.7
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)
11.71.76990.4842.4

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 REPLACEMENTTHROUGHOUT3C2X1.73507733770076370599.070.203470.202550.200270.24441RANDOM24.411
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]
1.82-1.03-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.858
r_dihedral_angle_4_deg15.506
r_dihedral_angle_3_deg12.508
r_dihedral_angle_1_deg5.055
r_scangle_it4.76
r_scbond_it3.268
r_mcangle_it2.305
r_angle_refined_deg1.926
r_mcbond_it1.492
r_chiral_restr0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.858
r_dihedral_angle_4_deg15.506
r_dihedral_angle_3_deg12.508
r_dihedral_angle_1_deg5.055
r_scangle_it4.76
r_scbond_it3.268
r_mcangle_it2.305
r_angle_refined_deg1.926
r_mcbond_it1.492
r_chiral_restr0.151
r_bond_refined_d0.024
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5348
Nucleic Acid Atoms
Solvent Atoms733
Heterogen Atoms54

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling