☰ Navigation Tabs
Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.6 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.946 α = 90 b = 101.32 β = 90 c = 82.019 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.8 40 95.8 0.108 6.4 5.7 26185 5.7
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 2.8 2.9 61.3 0.285 5.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B1Z 2.82 39.6 25045 2482 95.3 0.214 0.214 0.2834 RANDOM 31.1
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] -6 -0.19 6.19
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_angle_deg 1.3 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_angle_deg 1.3 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7034 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling