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Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with oxacillin
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 4.5 277 2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.56 65.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.415 α = 90 b = 100.415 β = 90 c = 189.799 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 2015-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97924 ALBA XALOC
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 2.7 86.79 99.7 0.137 0.078 0.99 8.5 3.8 30875
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 2.7 2.83 99.9 1.14 0.67 0.58 1.2 3.8
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 2.7 48.54 29554 1601 99.94 0.21985 0.21656 0.2068 0.28096 0.2562 RANDOM 63.405
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] 27.61 27.61 -55.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.904 r_dihedral_angle_3_deg 23.502 r_dihedral_angle_4_deg 18.886 r_dihedral_angle_1_deg 8.875 r_long_range_B_refined 5.493 r_long_range_B_other 5.493 r_scangle_other 4.387 r_mcangle_it 3.911 r_mcangle_other 3.91 r_scbond_it 3.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.904 r_dihedral_angle_3_deg 23.502 r_dihedral_angle_4_deg 18.886 r_dihedral_angle_1_deg 8.875 r_long_range_B_refined 5.493 r_long_range_B_other 5.493 r_scangle_other 4.387 r_mcangle_it 3.911 r_mcangle_other 3.91 r_scbond_it 3.368 r_scbond_other 3.365 r_mcbond_other 3.002 r_mcbond_it 3.001 r_angle_refined_deg 2.596 r_angle_other_deg 1.387 r_chiral_restr 0.151 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 4994 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building SCALA data scaling MOLREP phasing