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Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 10% PEG 3350 0.2M Sodium potassium tartrate 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.661 α = 90 b = 101.653 β = 90 c = 163.328 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 100 PIXEL DECTRIS PILATUS3 2M 2018-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.28 78.04 80.68 0.116 0.05 0.998 10.8 6.8 27481
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 100 0.828 0.35 0.907 2.5 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DWF 2.28 77.921 27481 1341 80.679 0.191 0.1877 0.1932 0.255 0.2613 26.517
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] -0.094 0.046 0.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 15.572 r_dihedral_angle_1_deg 7.548 r_lrange_it 5.732 r_lrange_other 5.732 r_scangle_it 3.473 r_scangle_other 3.472 r_mcangle_it 3 r_mcangle_other 2.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 15.572 r_dihedral_angle_1_deg 7.548 r_lrange_it 5.732 r_lrange_other 5.732 r_scangle_it 3.473 r_scangle_other 3.472 r_mcangle_it 3 r_mcangle_other 2.999 r_scbond_it 2.104 r_scbond_other 2.104 r_mcbond_other 1.775 r_mcbond_it 1.774 r_angle_refined_deg 1.432 r_angle_other_deg 1.269 r_nbd_refined 0.194 r_symmetry_nbd_other 0.194 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.159 r_symmetry_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5203 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing