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Crystal structure of penicillin-binding protein 2 from Yersinia pestis
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 1 uL of 1 mg/ml YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 2 uL reservoir solution (containing 0.1 M HEPES-NaOH pH 7.5, 0.5 M K+/Na+ tartrate and 10 mM NaBr)
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.661 α = 113.467 b = 84.773 β = 94.972 c = 88.359 γ = 103.725
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 PILATUS 6M 2018-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 79.36 90.2 0.133 0.163 0.095 0.781 6.7 5.5 56420
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 2.2 2.26 87.8 0.827 0.756 0.632 0.703 1.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LP4 2.26 50.005 52196 2616 90.395 0.194 0.1914 0.2525 0.2549 50.592
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] -2.724 -4.025 -3.875 0.136 1.946 2.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 20.905 r_dihedral_angle_3_deg 17.271 r_dihedral_angle_1_deg 11.411 r_lrange_it 9.728 r_lrange_other 9.714 r_scangle_it 7.002 r_scangle_other 7.002 r_mcangle_it 6.389 r_mcangle_other 6.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.256 r_dihedral_angle_4_deg 20.905 r_dihedral_angle_3_deg 17.271 r_dihedral_angle_1_deg 11.411 r_lrange_it 9.728 r_lrange_other 9.714 r_scangle_it 7.002 r_scangle_other 7.002 r_mcangle_it 6.389 r_mcangle_other 6.389 r_scbond_it 4.558 r_scbond_other 4.557 r_mcbond_it 4.272 r_mcbond_other 4.267 r_angle_refined_deg 1.554 r_angle_other_deg 1.222 r_symmetry_xyhbond_nbd_refined 0.296 r_nbd_other 0.248 r_nbd_refined 0.192 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.117 r_ncsr_local_group_1 0.101 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8420 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing