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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Cefditoren - Streptococcus pneumoniae R6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.941 α = 90 b = 149.052 β = 90 c = 98.802 γ = 90
Symmetry Space Group C 2 2 21
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 2M 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.639 48.48 97.8 0.077 0.998 10.01 4.29 85598 35.213
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.639 1.74 98.9 1.814 0.231 0.67 4.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.64 48.471 85598 2145 97.785 0.175 0.1738 0.1867 0.2035 0.2144 36.003
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] 0.64 -0.559 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.455 r_dihedral_angle_6_deg 15.653 r_dihedral_angle_3_deg 11.223 r_lrange_it 7.995 r_lrange_other 7.853 r_dihedral_angle_1_deg 6.547 r_scangle_it 5.469 r_scangle_other 5.468 r_scbond_it 3.602 r_scbond_other 3.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.455 r_dihedral_angle_6_deg 15.653 r_dihedral_angle_3_deg 11.223 r_lrange_it 7.995 r_lrange_other 7.853 r_dihedral_angle_1_deg 6.547 r_scangle_it 5.469 r_scangle_other 5.468 r_scbond_it 3.602 r_scbond_other 3.601 r_mcangle_other 2.361 r_mcangle_it 2.36 r_mcbond_it 1.755 r_mcbond_other 1.752 r_angle_refined_deg 1.272 r_angle_other_deg 0.446 r_nbd_refined 0.217 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.173 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.162 r_symmetry_nbd_refined 0.127 r_dihedral_angle_other_2_deg 0.101 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3514 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 60
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP/wARP model building Coot model building REFMAC refinement