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Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 290 2.3-3M NaCl, 0.1M Na Acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.75 67.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.839 α = 90 b = 100.839 β = 90 c = 189.354 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M-F 2015-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97497 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.85 48.72 100 0.192 0.078 9.3 6.9 26783
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 100 1.7 0.7 1.3 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 (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 1K25 2.85 87.33 25437 1303 99.94 0.17027 0.16729 0.171 0.22875 0.2297 RANDOM 70.969
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.736 r_dihedral_angle_3_deg 18.404 r_dihedral_angle_4_deg 15.256 r_long_range_B_other 10.596 r_long_range_B_refined 10.595 r_dihedral_angle_1_deg 8.259 r_mcangle_it 7.621 r_mcangle_other 7.62 r_scangle_other 7.606 r_scbond_it 5.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.736 r_dihedral_angle_3_deg 18.404 r_dihedral_angle_4_deg 15.256 r_long_range_B_other 10.596 r_long_range_B_refined 10.595 r_dihedral_angle_1_deg 8.259 r_mcangle_it 7.621 r_mcangle_other 7.62 r_scangle_other 7.606 r_scbond_it 5.309 r_scbond_other 5.292 r_mcbond_it 5.146 r_mcbond_other 5.144 r_angle_refined_deg 1.761 r_angle_other_deg 1.069 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 5178 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing