☰ Navigation Tabs
Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000).
The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.172 α = 112.917 b = 84.035 β = 95.306 c = 87.099 γ = 104.566
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 PILATUS3 X 2M 2018-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.8 45.693 92.9 0.108 0.097 0.991 4.1 2.1 27215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 96.7 0.452 0.64 0.452 0.677 1.2 2.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LP4 2.8 45.693 27076 1308 92.432 0.231 0.228 0.2902 0.271 66.303
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] -4.63 -8.426 -6.118 1.424 4.642 3.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_3_deg 18.661 r_dihedral_angle_4_deg 16.094 r_lrange_it 8.632 r_lrange_other 8.631 r_dihedral_angle_1_deg 6.78 r_mcangle_it 5.33 r_mcangle_other 5.329 r_scangle_it 4.728 r_scangle_other 4.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.136 r_dihedral_angle_3_deg 18.661 r_dihedral_angle_4_deg 16.094 r_lrange_it 8.632 r_lrange_other 8.631 r_dihedral_angle_1_deg 6.78 r_mcangle_it 5.33 r_mcangle_other 5.329 r_scangle_it 4.728 r_scangle_other 4.727 r_mcbond_it 3.202 r_mcbond_other 3.202 r_scbond_it 2.711 r_scbond_other 2.711 r_angle_refined_deg 1.299 r_angle_other_deg 1.091 r_symmetry_xyhbond_nbd_refined 0.247 r_nbd_other 0.237 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.195 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.121 r_ncsr_local_group_1 0.095 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.046 r_chiral_restr_other 0.035 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 8166 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing