☰ Navigation Tabs
Crystal structure of peptidase B from Yersinia pestis CO92 at 2.75 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IJ3 PDB entry 3IJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 uL 14 mg/mL protein in 20 mM Tris-HCl pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 1 mM ZnCl2 + 0.2 uL TOP96 #29 (0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% w/v PEG8000) against 1.5 M sodium chloride, 96-well 3-drop crystallization plate (Swissci)
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.558 α = 90 b = 101.558 β = 90 c = 240.475 γ = 120
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 MARMOSAIC 300 mm CCD 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.75 50 99.5 0.152 0.152 16.5 10.8 12769 -3 60.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 94.8 0.666 0.666 0.928 1.8 5.9
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 PDB entry 3IJ3 2.75 50 11976 600 98.5 0.18097 0.17761 0.1851 0.24925 0.2506 RANDOM 53.504
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] 0.54 0.27 0.54 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.706 r_dihedral_angle_3_deg 14.099 r_dihedral_angle_4_deg 11.756 r_long_range_B_other 8.322 r_long_range_B_refined 8.319 r_dihedral_angle_1_deg 5.853 r_scangle_other 5.746 r_mcangle_other 5.28 r_mcangle_it 5.277 r_scbond_it 4.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.706 r_dihedral_angle_3_deg 14.099 r_dihedral_angle_4_deg 11.756 r_long_range_B_other 8.322 r_long_range_B_refined 8.319 r_dihedral_angle_1_deg 5.853 r_scangle_other 5.746 r_mcangle_other 5.28 r_mcangle_it 5.277 r_scbond_it 4.208 r_scbond_other 3.792 r_mcbond_it 3.478 r_mcbond_other 3.464 r_angle_refined_deg 1.032 r_angle_other_deg 0.728 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3163 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction DENZO data reduction HKL-3000 data scaling SCALEPACK data scaling HKL-3000 phasing MOLREP phasing PDB_EXTRACT data extraction