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Crystal structure of PHAB8, a peptidoglycan hydrolase with relatively weak thermal stability and broad-spectrum.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ET6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 3% w/v Dextran sulfate sodium salt, 0.1 M bicine pH 8.5, 15% w/v Polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.03 α = 90 b = 156.98 β = 90 c = 47.26 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 81 CCD MARMOSAIC 225 mm CCD 2021-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
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 2.4 35.29 99.6 0.218 0.996 9.5 12.9 11885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 0.585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.4 35.29 0.3 11276 1128 94.62 0.2395 0.2359 0.2523 0.2707 0.285
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 6.281 f_angle_d 0.944 f_chiral_restr 0.047 f_plane_restr 0.011 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1505 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 17
Software Software Software Name Purpose xia2 data scaling PHENIX refinement XDS data reduction HKL-3000 phasing