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Crystal structure of the complex of short peptidoglycan recognition protein from Camelus dromedarius with nonanoic acid at 1.83 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 3350 Sodium potassium tartarate
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.775 α = 90 b = 101.525 β = 90 c = 163.087 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 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.99 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 1.83 50 99.8 0.06 2 4.3 64628 2
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 1.83 1.86 0.43 2 4.3
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 THROUGHOUT 1.834 34.256 64627 1288 99.751 0.273 0.272 0.2774 0.3211 0.3286 32.334
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] 2.218 -2.616 0.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.298 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_2_deg 8.059 r_lrange_it 7.814 r_lrange_other 7.808 r_dihedral_angle_1_deg 6.82 r_scangle_it 5.165 r_scangle_other 5.165 r_mcangle_it 4.275 r_mcangle_other 4.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.298 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_2_deg 8.059 r_lrange_it 7.814 r_lrange_other 7.808 r_dihedral_angle_1_deg 6.82 r_scangle_it 5.165 r_scangle_other 5.165 r_mcangle_it 4.275 r_mcangle_other 4.275 r_scbond_it 3.334 r_scbond_other 3.334 r_mcbond_it 2.847 r_mcbond_other 2.847 r_angle_refined_deg 1.436 r_angle_other_deg 0.515 r_symmetry_nbd_refined 0.261 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.22 r_nbd_refined 0.214 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.18 r_ncsr_local_group_3 0.104 r_ncsr_local_group_5 0.103 r_ncsr_local_group_1 0.102 r_ncsr_local_group_2 0.096 r_ncsr_local_group_4 0.09 r_ncsr_local_group_6 0.086 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5203 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling autoPROC data processing PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing