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Crystal structure of peptidoglycan recognition protein (PGRP-S) at 2.45 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 7.2 290 0.3M NaKTartrate, 25% PEG, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.47 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.788 α = 90 b = 101.796 β = 90 c = 164.144 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 CCD MARRESEARCH Mirror 2016-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 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 2.45 86.51 94 0.2 6.74 4.1 26675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 71.7 0.825 1.315 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Q8S 2.45 86.51 26675 1362 99.88 0.23661 0.23372 0.29361 0.2554 RANDOM 55.18
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] 8.48 -5.19 -3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.661 r_long_range_B_refined 13.897 r_dihedral_angle_3_deg 13.833 r_long_range_B_other 13.833 r_dihedral_angle_4_deg 11.642 r_scangle_other 7.87 r_mcangle_it 7.408 r_mcangle_other 7.407 r_dihedral_angle_1_deg 6.269 r_scbond_it 4.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.661 r_long_range_B_refined 13.897 r_dihedral_angle_3_deg 13.833 r_long_range_B_other 13.833 r_dihedral_angle_4_deg 11.642 r_scangle_other 7.87 r_mcangle_it 7.408 r_mcangle_other 7.407 r_dihedral_angle_1_deg 6.269 r_scbond_it 4.863 r_scbond_other 4.858 r_mcbond_it 4.519 r_mcbond_other 4.518 r_angle_refined_deg 1.538 r_angle_other_deg 1.034 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 5347 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing