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Crystal structure of Staphylococcal superantigen-like protein SAOUHSC_00383
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 6% TACSIMATE pH 6.0, 25% (W/V) PEG 3350 , 0.1M MES pH 6.0, 0.1M NDSB-256, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.9 α = 90 b = 70.5 β = 106.2 c = 126.5 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 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2013-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 121.477 99.4 0.061 20.3 4.3 45615 45615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63 98.7 0.393 0.393 0.449 0.215 2 4.3 6561
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 2RDG 2.5 19.69 45608 2300 99.37 0.2091 0.2052 0.2088 0.2835 0.2809 RANDOM 45.573
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] 0.49 2.65 -3.62 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.488 r_dihedral_angle_4_deg 23.826 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 8.888 r_angle_refined_deg 1.635 r_angle_other_deg 0.844 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.488 r_dihedral_angle_4_deg 23.826 r_dihedral_angle_3_deg 18.697 r_dihedral_angle_1_deg 8.888 r_angle_refined_deg 1.635 r_angle_other_deg 0.844 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9046 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction