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The structure of the variable domain of Streptococcus intermedius antigen I/II (Pas)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 25% PEG3350, 250mM MgCl2, 100mM Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.038 α = 90 b = 91.308 β = 116.78 c = 71.893 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 MARMOSAIC 300 mm CCD Si 111 2017-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 45.65 98.9 0.074 0.09 0.051 0.993 8.5 3 88963 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.8 0.927 1.137 0.648 0.583 1.6 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WD6 1.7 45.65 84631 4304 98.84 0.219 0.2175 0.247 0.2778 RANDOM 38.895
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] -2.51 -1.04 -0.93 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.849 r_dihedral_angle_3_deg 12.784 r_dihedral_angle_4_deg 12.573 r_dihedral_angle_1_deg 6.588 r_angle_refined_deg 1.504 r_angle_other_deg 0.938 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.849 r_dihedral_angle_3_deg 12.784 r_dihedral_angle_4_deg 12.573 r_dihedral_angle_1_deg 6.588 r_angle_refined_deg 1.504 r_angle_other_deg 0.938 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6135 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing