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Crystal structure of PBP3 transpeptidase domain from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 14.4 mg/ml PBP3, 0.1 M sodium cacodylate, 5% (w/v) PEG 8000, 20% (v/v) MPD, 0.2% (w/v) betaine, 0.2% (w/v) L-glutamic acid, 0.2% (w/v) L-proline, 0.2% (w/v) taurine, 0.2% (w/v) trimethlyamin N-oxide, 0.02 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.28 α = 90 b = 109.28 β = 90 c = 143.229 γ = 120
Symmetry Space Group P 62 2 2
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-F 2019-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.298 47.743 93.9 0.103 0.999 20.7 17.8 9457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.298 2.603 74.6 1.456 0.84 2.4 15.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4BJP 2.3 47.74 1.34 9456 469 40.84 0.2321 0.2295 0.2294 0.282 0.2845 66.52
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.2638 f_angle_d 0.4027 f_chiral_restr 0.0398 f_plane_restr 0.0037 f_bond_d 0.0014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3001 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction STARANISO data processing