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Crystal structure of a peptidoglycan release complex, SagB-SpdC, in lipidic cubic phase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 298 24-32% PEG400, 0.5M ammonium sulfate, 100mM sodium citrate or sodium acetate pH 4.4-5.0 (4.6 optimal), 35 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 3.23 61.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.669 α = 90 b = 54.758 β = 107.18 c = 96.418 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 16M 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.6 46.98 99.3 0.15 0.097 0.994 4.7 5.8 24207 71.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.71 97.2 1.669 0.53 0.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6fxp 2.6 46.98 1.34 24046 1763 98.66 0.2546 0.2527 0.2525 0.2792 0.2789 random selection 98.66
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 13.164 f_angle_d 0.478 f_chiral_restr 0.0391 f_plane_restr 0.0026 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4233 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building