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Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 20% glycerol, 6% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.535 α = 90 b = 101.56 β = 90 c = 163.457 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH mirror 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 50 97.7 0.143 15.5 23666 23666 53.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 84.7 0.59 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3C2X 2.5 39.74 23666 23666 1198 95 0.211 0.21 0.21 0.2073 0.231 0.2458 RANDOM 51.1
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] 35.18 -22.86 -12.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_angle_deg 2.1 c_improper_angle_d 1.34 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 61
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling