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Crystal structure of S. aureus DivIVA N terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Carboxylic acids, 0.1 M Buffer system 1 pH 6.5, 37.5 % v/v MPD_P1K_P3350; Morpheus G4
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.108 α = 90 b = 39.175 β = 90 c = 111.249 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 PILATUS3 6M 2018-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
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 1.3 37.08 100 0.087 0.101 0.051 0.99 10.9 6.9 31216 15.87
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 1.3 1.32 99.6 0.556 0.653 0.339 0.904 2.5 6.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WUJ 1.3 36.95 1.38 31123 1506 99.87 0.1612 0.1601 0.1636 0.1848 0.1874 23.98
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 3.464 f_angle_d 0.747 f_chiral_restr 0.0602 f_plane_restr 0.0074 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 822 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing