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Crystal structure of Staphylococcal Superantigen-Like protein 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M4V PDB ENTRY 1M4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M PEG3350, 0.2M NaH2PO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.391 α = 90 b = 98.152 β = 91.47 c = 79.515 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97907 SSRL BL9-1
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 1.7 30.89 94 0.028 3.8 86026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 71.5 0.463 3 3.3 6500
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 PDB ENTRY 1M4V 1.7 30.89 85991 4300 93.93 0.19461 0.1923 0.191 0.23878 0.2375 RANDOM 31.391
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] 0.14 0.05 -0.12 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_1_deg 6.184 r_scangle_it 3.686 r_scbond_it 2.368 r_mcangle_it 1.484 r_angle_refined_deg 1.426 r_mcbond_it 0.859 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_4_deg 13.855 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_1_deg 6.184 r_scangle_it 3.686 r_scbond_it 2.368 r_mcangle_it 1.484 r_angle_refined_deg 1.426 r_mcbond_it 0.859 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.131 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6172 Nucleic Acid Atoms Solvent Atoms 737 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing