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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Ampicillin - 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 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.275 α = 90 b = 148.859 β = 90 c = 99.386 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 2021-02-01 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 1.788 48.14 99.4 0.087 0.996 8.82 4.32 66996 39.987
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 1.788 1.9 99.7 1.221 0.479 1.2 4.49
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 1.79 48.138 66996 2052 99.368 0.169 0.1679 0.1784 0.189 0.2008 40.046
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] -0.111 0.391 -0.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.398 r_dihedral_angle_3_deg 11.27 r_lrange_it 8.179 r_lrange_other 8.137 r_scangle_it 7.195 r_scangle_other 7.194 r_dihedral_angle_1_deg 6.328 r_dihedral_angle_2_deg 5.872 r_scbond_it 4.646 r_scbond_other 4.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.398 r_dihedral_angle_3_deg 11.27 r_lrange_it 8.179 r_lrange_other 8.137 r_scangle_it 7.195 r_scangle_other 7.194 r_dihedral_angle_1_deg 6.328 r_dihedral_angle_2_deg 5.872 r_scbond_it 4.646 r_scbond_other 4.645 r_mcangle_other 3.447 r_mcangle_it 3.446 r_mcbond_it 2.605 r_mcbond_other 2.605 r_angle_refined_deg 1.202 r_angle_other_deg 0.422 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbd_other 0.189 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.066 r_gen_planes_refined 0.007 r_bond_refined_d 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 3506 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 46
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP/wARP model building Coot model building REFMAC refinement