☰ Navigation Tabs
Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 296 Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5).
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.265 α = 90 b = 147.772 β = 90 c = 164.523 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.67 109.937 100 0.133 0.999 12.2 13.1 38541
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.701 7.331 0.04 0.999
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6TII 2.673 109.937 30718 1485 77.249 0.216 0.213 0.2162 0.2851 0.2832 77.799
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] 0.278 0.125 -0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.947 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 9.792 r_lrange_it 8.551 r_lrange_other 8.51 r_mcangle_it 5.381 r_mcangle_other 5.38 r_scangle_it 4.707 r_scangle_other 4.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.947 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 17.737 r_dihedral_angle_1_deg 9.792 r_lrange_it 8.551 r_lrange_other 8.51 r_mcangle_it 5.381 r_mcangle_other 5.38 r_scangle_it 4.707 r_scangle_other 4.707 r_mcbond_it 3.194 r_mcbond_other 3.191 r_scbond_other 2.659 r_scbond_it 2.658 r_angle_refined_deg 1.279 r_angle_other_deg 1.102 r_nbd_other 0.244 r_nbd_refined 0.195 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.157 r_chiral_restr_other 0.118 r_ncsr_local_group_1 0.112 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.077 r_symmetry_xyhbond_nbd_refined 0.069 r_chiral_restr 0.053 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8499 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASES phasing