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Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae with a bound phosphate at the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U3T PDB entry 4U3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.3 291 40% PEG600, 0.1 M CHES
Crystal Properties Matthews coefficient Solvent content 1.98 37.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.973 α = 90 b = 76.868 β = 92.32 c = 86.47 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.83 38.35 99.6 0.071 0.029 0.678 42.5 6.8 48725 30
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 1.83 1.86 99.2 0.932 0.394 0.764 2 6.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4U3T 1.83 38.35 46252 2436 98.4 0.197 0.195 0.2016 0.233 0.2419 RANDOM 37.5
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] 0.43 0.26 -0.04 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.565 r_dihedral_angle_4_deg 15.053 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 6.064 r_long_range_B_refined 4.932 r_long_range_B_other 4.878 r_scangle_other 3.627 r_mcangle_it 2.68 r_mcangle_other 2.68 r_scbond_it 2.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.565 r_dihedral_angle_4_deg 15.053 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 6.064 r_long_range_B_refined 4.932 r_long_range_B_other 4.878 r_scangle_other 3.627 r_mcangle_it 2.68 r_mcangle_other 2.68 r_scbond_it 2.263 r_scbond_other 2.255 r_mcbond_it 1.874 r_mcbond_other 1.872 r_angle_refined_deg 1.269 r_angle_other_deg 0.761 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4747 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing