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Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of Streptococcus pyogenes SfbI-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RKZ PDB ENTRY 2RKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 CRYSTALS OF THE PROTEIN/PEPTIDE COMPLEX (0.3 MM/3.5 MM, PH 7.7) WERE GROWN USING SITTING DROP VAPOUR DIFFUSION FROM A 1:1 DILUTION WITH WELL SOLUTION (0.1 M TRIS PH 7.0, 1.5 M (NH4)2SO4 AT 18 DEGREES CENTIGRADE
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.055 α = 90 b = 50.055 β = 90 c = 93.504 γ = 90
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 CCD BENT CYLINDRICAL MIRRORS 2008-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 28.22 100 0.05 22.4 6.1 25333 1.9 22.64
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 1.79 100 0.41 3.6 6.1
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 PDB ENTRY 2RKZ 1.7 26.45 24001 1289 99.98 0.17621 0.17389 0.22157 0.2365 RANDOM 23.575
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] -0.38 -0.38 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.26 r_dihedral_angle_4_deg 14.966 r_dihedral_angle_3_deg 10.656 r_dihedral_angle_1_deg 5.862 r_scangle_it 3.7 r_scbond_it 2.334 r_mcangle_it 1.535 r_angle_refined_deg 1.353 r_mcbond_it 0.871 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.26 r_dihedral_angle_4_deg 14.966 r_dihedral_angle_3_deg 10.656 r_dihedral_angle_1_deg 5.862 r_scangle_it 3.7 r_scbond_it 2.334 r_mcangle_it 1.535 r_angle_refined_deg 1.353 r_mcbond_it 0.871 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.191 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_other r_mcangle_other r_scbond_other 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 1628 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing