☰ Navigation Tabs
PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Penicillin G - 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 3.3 62.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.743 α = 90 b = 149.377 β = 90 c = 98.421 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 2021-10-09 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 1.509 43.42 98.4 0.059 0.998 10.08 4.5 109659 38.303
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 1.509 1.6 97.3 2.08 0.227 0.64 4.2
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 1.51 43.412 109644 2188 98.361 0.163 0.1629 0.1764 0.1903 0.2 40.025
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] 0.538 -0.248 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.525 r_dihedral_angle_3_deg 11.745 r_lrange_it 7.963 r_lrange_other 7.851 r_dihedral_angle_2_deg 7.074 r_dihedral_angle_1_deg 6.673 r_scangle_it 5.736 r_scangle_other 5.735 r_scbond_it 3.764 r_scbond_other 3.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.525 r_dihedral_angle_3_deg 11.745 r_lrange_it 7.963 r_lrange_other 7.851 r_dihedral_angle_2_deg 7.074 r_dihedral_angle_1_deg 6.673 r_scangle_it 5.736 r_scangle_other 5.735 r_scbond_it 3.764 r_scbond_other 3.763 r_mcangle_other 3.024 r_mcangle_it 3.023 r_mcbond_it 2.143 r_mcbond_other 2.143 r_angle_refined_deg 1.293 r_angle_other_deg 0.454 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.185 r_nbd_other 0.145 r_xyhbond_nbd_refined 0.135 r_symmetry_nbd_refined 0.13 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3624 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 50
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP/wARP model building Coot model building REFMAC refinement