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Crystal Structure of LPXTG-motif Cell Wall Anchor Domain Protein MSCRAMM_SdrD from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.16 M magnesium chloride, 0.08 TrisHCl pH8.5, 24 %(w/v) PEG4000, 20 % (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.054 α = 90 b = 72.825 β = 90 c = 148.453 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2023-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 29.33 99.8 0.085 0.092 0.025 0.999 17 13.4 44004 26.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 98 0.791 0.824 0.228 0.9 2.9 12.7
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 FREE R-VALUE 1.8 29.33 1.36 43927 2124 99.84 0.18 0.1785 0.1785 0.2109 0.2109 34.95
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 13.0546 f_angle_d 0.6564 f_chiral_restr 0.0518 f_plane_restr 0.0044 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3349 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling HKL-3000 phasing MOLREP phasing