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Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.67 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 2.43 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.583 α = 90 b = 101.026 β = 90 c = 163.412 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 2.67 85.93 91.49 0.113 0.06 0.994 12.6 4.4 19639
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 2.67 2.71 90 0.718 0.367 0.776 4.6 4.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DWF 2.67 85.93 19639 961 91.502 0.18 0.1754 0.2657 0.2458 33.021
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] -0.176 0.169 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.448 r_dihedral_angle_4_deg 19.928 r_dihedral_angle_3_deg 18.936 r_lrange_it 10.033 r_lrange_other 10.033 r_dihedral_angle_1_deg 7.788 r_scangle_it 5.631 r_scangle_other 5.63 r_mcangle_it 4.786 r_mcangle_other 4.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.448 r_dihedral_angle_4_deg 19.928 r_dihedral_angle_3_deg 18.936 r_lrange_it 10.033 r_lrange_other 10.033 r_dihedral_angle_1_deg 7.788 r_scangle_it 5.631 r_scangle_other 5.63 r_mcangle_it 4.786 r_mcangle_other 4.786 r_scbond_it 3.592 r_scbond_other 3.591 r_mcbond_it 3.053 r_mcbond_other 3.049 r_angle_refined_deg 1.65 r_angle_other_deg 1.264 r_symmetry_nbd_refined 0.22 r_symmetry_nbd_other 0.206 r_nbd_refined 0.203 r_nbd_other 0.2 r_xyhbond_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5203 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing