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Non-canonical Staphylococcus aureus pathogenicity island repression
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1 M Tris-HCl pH 8.5, 22 % PEG350
Crystal Properties Matthews coefficient Solvent content 3.57 65.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.218 α = 90 b = 88.218 β = 90 c = 110.489 γ = 120
Symmetry Space Group P 32 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 288 PIXEL DECTRIS PILATUS 6M-F 2018-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.973 62.919 83.7 0.999 12.3 9.8 8900
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 2.973 3.167 0.487
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7P4A 2.973 62.919 8900 415 83.623 0.251 0.2488 0.295 0.2877 97.47
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] 0.022 0.011 0.022 -0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_4_deg 11.276 r_lrange_it 7.689 r_lrange_other 7.688 r_dihedral_angle_1_deg 6.308 r_mcangle_other 4.656 r_mcangle_it 4.654 r_scangle_it 3.98 r_scangle_other 3.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.623 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_4_deg 11.276 r_lrange_it 7.689 r_lrange_other 7.688 r_dihedral_angle_1_deg 6.308 r_mcangle_other 4.656 r_mcangle_it 4.654 r_scangle_it 3.98 r_scangle_other 3.979 r_mcbond_it 2.726 r_mcbond_other 2.702 r_scbond_it 2.225 r_scbond_other 2.224 r_angle_refined_deg 1.154 r_angle_other_deg 1.036 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.188 r_nbd_other 0.169 r_symmetry_nbd_other 0.167 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2424 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction AutoProcess data scaling PHASER phasing