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Salmonella effector SpvD - G161 variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 100 mM Tris, 200 mM NaCl, 22 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44 α = 90 b = 51.97 β = 107.7 c = 47.22 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2015-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 51.97 99.4 0.104 10.4 5.9 26737
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 1.6 1.69 99.2 0.579 1.9 6
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 (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 THROUGHOUT 5LQ6 1.6 44.98 25387 1333 99.23 0.1649 0.16319 0.1741 0.1973 0.2057 RANDOM 20.415
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] 0.21 -0.73 -0.24 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_4_deg 9.048 r_long_range_B_refined 7.76 r_long_range_B_other 7.758 r_scangle_other 6.2 r_dihedral_angle_1_deg 5.835 r_scbond_it 4.026 r_scbond_other 4.021 r_mcangle_it 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.51 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_4_deg 9.048 r_long_range_B_refined 7.76 r_long_range_B_other 7.758 r_scangle_other 6.2 r_dihedral_angle_1_deg 5.835 r_scbond_it 4.026 r_scbond_other 4.021 r_mcangle_it 3.256 r_mcangle_other 3.255 r_mcbond_it 2.225 r_mcbond_other 2.224 r_angle_refined_deg 1.41 r_angle_other_deg 0.987 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1664 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing