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Crystal structure of A. baumannii penicillin-binding protein 2
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, SITTING DROP 4.2 291 0.1M Na2HPO4 adjusted to pH 4.2 with citric acid, 16% (v/v) ethanol, and 5% (w/v) PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.249 α = 90 b = 151.03 β = 90 c = 177.369 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 PIXEL DECTRIS PILATUS3 6M 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.65 44.34 98.7 0.203 0.213 0.065 0.994 9 9.7 46823
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 2.65 2.74 99.4 1.108 1.167 0.36 0.754 2 9.7
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 5LP4 2.65 44.334 46819 2395 98.388 0.213 0.211 0.2236 0.2523 0.2642 61.653
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] 9 -2.868 -6.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_3_deg 17.275 r_dihedral_angle_4_deg 14.104 r_lrange_other 9.799 r_lrange_it 9.798 r_mcangle_it 7.272 r_mcangle_other 7.272 r_dihedral_angle_1_deg 7.052 r_scangle_it 6.681 r_scangle_other 6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_3_deg 17.275 r_dihedral_angle_4_deg 14.104 r_lrange_other 9.799 r_lrange_it 9.798 r_mcangle_it 7.272 r_mcangle_other 7.272 r_dihedral_angle_1_deg 7.052 r_scangle_it 6.681 r_scangle_other 6.68 r_mcbond_it 4.552 r_mcbond_other 4.552 r_scbond_it 4.042 r_scbond_other 4.041 r_angle_refined_deg 1.525 r_angle_other_deg 1.195 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.171 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_other 0.148 r_nbd_other 0.124 r_ncsr_local_group_1 0.09 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_refined 0.074 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8071 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing