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Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 10% PEG 3350,
0.2M Sodium potassium tartarate
Crystal Properties Matthews coefficient Solvent content 2.43 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.5 α = 90 b = 101.37 β = 90 c = 163.04 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 298 PIXEL DECTRIS PILATUS3 6M 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.11 86.09 100 0.09 0.1 3.05 6.6 42613 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.17 100 0.74 0.81 6.3
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 (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 4Q8S 2.11 86.09 40430 2161 99.95 0.19365 0.19067 0.2 0.24884 0.2541 RANDOM 47.707
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] 5.65 -4.09 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.263 r_dihedral_angle_4_deg 15.17 r_dihedral_angle_3_deg 13.937 r_long_range_B_refined 8.554 r_long_range_B_other 8.553 r_dihedral_angle_1_deg 7.304 r_scangle_other 6.601 r_mcangle_it 5.066 r_mcangle_other 5.066 r_scbond_it 4.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.263 r_dihedral_angle_4_deg 15.17 r_dihedral_angle_3_deg 13.937 r_long_range_B_refined 8.554 r_long_range_B_other 8.553 r_dihedral_angle_1_deg 7.304 r_scangle_other 6.601 r_mcangle_it 5.066 r_mcangle_other 5.066 r_scbond_it 4.481 r_scbond_other 4.481 r_mcbond_it 3.59 r_mcbond_other 3.59 r_angle_refined_deg 1.766 r_angle_other_deg 1.073 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5223 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing