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A fragment of streptococcal M1 protein in complex with human fibrinogen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E1I PDB ENTRY 3E1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.3 M AMMONIUM TARTRATE, 0.1 M MES, PH 6.25.
Crystal Properties Matthews coefficient Solvent content 5.86 79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.687 α = 90 b = 165.687 β = 90 c = 289.652 γ = 120
Symmetry Space Group P 32 2 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 225 mm CCD 2009-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
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 6 142.8 92.1 0.19 7.7 4 5481 1.8
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 7.5 7.7 56.3 0.33 1.8 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3E1I 7.5 142.86 5481 286 92.1 0.423 0.424 0.4226 0.408 0.4325 RANDOM 34.54
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] 11.56 5.78 11.56 -17.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.321 r_dihedral_angle_3_deg 15.536 r_dihedral_angle_4_deg 12.86 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.186 r_symmetry_vdw_refined 0.803 r_symmetry_hbond_refined 0.466 r_nbd_refined 0.333 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.321 r_dihedral_angle_3_deg 15.536 r_dihedral_angle_4_deg 12.86 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.186 r_symmetry_vdw_refined 0.803 r_symmetry_hbond_refined 0.466 r_nbd_refined 0.333 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.29 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10956 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing