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Crystal structure of Y. pestis penicillin-binding protein 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000)
Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000
Crystal Properties Matthews coefficient Solvent content 3.47 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.8 α = 90 b = 100.8 β = 90 c = 314.409 γ = 90
Symmetry Space Group P 41 21 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 PILATUS 6M-F 2018-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9196 Diamond I04-1
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 3 29.64 99.9 0.2 0.071 0.997 9.1 10 33546 50.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.15 100 1.099 0.518 0.941 1.4
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 6SYN 3 29.64 33459 1713 99.836 0.245 0.2439 0.2483 0.2764 0.2793 82.519
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] 7.716 7.716 -15.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.564 r_dihedral_angle_3_deg 16.545 r_dihedral_angle_4_deg 12.879 r_dihedral_angle_1_deg 5.288 r_lrange_it 4.756 r_lrange_other 4.756 r_mcangle_it 2.861 r_mcangle_other 2.861 r_scangle_it 2.069 r_scangle_other 2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.564 r_dihedral_angle_3_deg 16.545 r_dihedral_angle_4_deg 12.879 r_dihedral_angle_1_deg 5.288 r_lrange_it 4.756 r_lrange_other 4.756 r_mcangle_it 2.861 r_mcangle_other 2.861 r_scangle_it 2.069 r_scangle_other 2.069 r_mcbond_it 1.576 r_mcbond_other 1.573 r_angle_refined_deg 1.197 r_scbond_it 1.069 r_scbond_other 1.069 r_angle_other_deg 1.029 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_other 0.184 r_symmetry_nbd_refined 0.182 r_symmetry_nbd_other 0.172 r_nbd_refined 0.167 r_nbtor_refined 0.146 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.033 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7019 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing