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Crystal structure of camel peptidoglycan recognition protein, PGRP-S with a trapped diethylene glycol in the ligand diffusion channel at 3.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 0.2M SODIUM POTASSIUM TARTRATE, 10% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.54 α = 90 b = 100.596 β = 90 c = 163.139 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 2010-10-21 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 3.2 42.35 97.8 0.125 15 12236 12236 47.7
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 3.2 3.26 92.8 0.356 3.7
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 3OLK 3.2 42.35 12138 12138 618 97.1 0.21 0.21 0.21 0.2018 0.248 0.2513 RANDOM 31.4
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 -0.29 1.82
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.9 c_angle_deg 1.7 c_improper_angle_d 1.14 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling