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PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (22)
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 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.473 α = 90 b = 148.153 β = 90 c = 97.962 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 6M 2024-06-25 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 1.52 48.74 93.5 0.039 0.999 13.28 3.8 101655 40.41
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 1.52 1.61 81.6 0.188 0.202 0.57 3.2
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 1.52 48.736 101584 2020 93.415 0.183 0.183 0.1962 0.201 0.2103 43.159
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] 1.04 -0.333 -0.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.046 r_dihedral_angle_3_deg 10.932 r_lrange_it 9.043 r_lrange_other 8.967 r_dihedral_angle_1_deg 6.502 r_scangle_it 6.302 r_scangle_other 6.301 r_dihedral_angle_2_deg 5.441 r_scbond_it 4.316 r_scbond_other 4.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.046 r_dihedral_angle_3_deg 10.932 r_lrange_it 9.043 r_lrange_other 8.967 r_dihedral_angle_1_deg 6.502 r_scangle_it 6.302 r_scangle_other 6.301 r_dihedral_angle_2_deg 5.441 r_scbond_it 4.316 r_scbond_other 4.315 r_mcangle_it 3.14 r_mcangle_other 3.14 r_mcbond_it 2.246 r_mcbond_other 2.245 r_dihedral_angle_other_2_deg 1.348 r_angle_refined_deg 1.294 r_angle_other_deg 0.447 r_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_other 0.212 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.167 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 3624 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing