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Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.07 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 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.889 α = 90 b = 101.508 β = 90 c = 162.996 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 0.97 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.07 46.36 99.82 0.041 0.99 8.13 6.94 45175
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 99.79 0.433 0.869 1.9 6
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 2.07 46.358 45174 1297 99.817 0.202 0.1998 0.2077 0.2576 0.2625 36.53
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] 0.018 -0.021 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_4_deg 14.04 r_dihedral_angle_1_deg 7.39 r_lrange_it 6.74 r_lrange_other 6.738 r_scangle_it 4.877 r_scangle_other 4.877 r_mcangle_it 3.878 r_mcangle_other 3.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_4_deg 14.04 r_dihedral_angle_1_deg 7.39 r_lrange_it 6.74 r_lrange_other 6.738 r_scangle_it 4.877 r_scangle_other 4.877 r_mcangle_it 3.878 r_mcangle_other 3.877 r_scbond_it 3.157 r_scbond_other 3.156 r_mcbond_it 2.71 r_mcbond_other 2.709 r_angle_refined_deg 1.498 r_angle_other_deg 1.351 r_symmetry_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.2 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.188 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 467 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing