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Crystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 20% glycerol, 6% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.308 α = 90 b = 101.623 β = 90 c = 162.683 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 77 CCD MARRESEARCH 2014-02-12 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 2.305 40.704 89.2 0.074 9.8 1 29076 44.6
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 2.305 2.34 0.668
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.305 40.704 29076 700 88.909 0.216 0.2147 0.2198 0.2833 0.2815 55.996
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] 7.997 -6.24 -1.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.914 r_dihedral_angle_3_deg 13.842 r_lrange_it 10.513 r_lrange_other 10.512 r_dihedral_angle_1_deg 7.574 r_scangle_it 6.004 r_scangle_other 6.002 r_mcangle_it 5.718 r_mcangle_other 5.718 r_dihedral_angle_2_deg 5.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.914 r_dihedral_angle_3_deg 13.842 r_lrange_it 10.513 r_lrange_other 10.512 r_dihedral_angle_1_deg 7.574 r_scangle_it 6.004 r_scangle_other 6.002 r_mcangle_it 5.718 r_mcangle_other 5.718 r_dihedral_angle_2_deg 5.118 r_scbond_it 3.596 r_scbond_other 3.594 r_mcbond_it 3.467 r_mcbond_other 3.466 r_angle_refined_deg 1.235 r_angle_other_deg 0.448 r_symmetry_nbd_other 0.215 r_nbd_refined 0.211 r_nbd_other 0.21 r_symmetry_nbd_refined 0.205 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.062 r_chiral_restr 0.059 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection AMoRE phasing DENZO data reduction SCALEPACK data scaling Coot model building