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Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 12% PEG 3350, 100mM Sodium potassium tartarate
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.309 α = 90 b = 101.149 β = 90 c = 163.566 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 2018-05-13 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 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 47.99 100 0.27 4.27 6.88 12435
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 3.2 3.28 100 0.63 0.35
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 3RT4 3.2 47.99 11977 458 99.94 0.19478 0.19193 0.1967 0.2654 0.2695 RANDOM 75.203
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] 15.73 -10.48 -5.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_mcangle_it 16.337 r_mcangle_other 16.335 r_dihedral_angle_3_deg 15.251 r_long_range_B_refined 14.492 r_long_range_B_other 14.474 r_dihedral_angle_4_deg 13.765 r_scangle_other 10.377 r_mcbond_other 10.19 r_mcbond_it 10.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_mcangle_it 16.337 r_mcangle_other 16.335 r_dihedral_angle_3_deg 15.251 r_long_range_B_refined 14.492 r_long_range_B_other 14.474 r_dihedral_angle_4_deg 13.765 r_scangle_other 10.377 r_mcbond_other 10.19 r_mcbond_it 10.188 r_scbond_other 9.869 r_scbond_it 9.864 r_dihedral_angle_1_deg 7.054 r_angle_other_deg 2.077 r_angle_refined_deg 1.4 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 5200 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing