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Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement fragment C3d revealing an alternative binding mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3D PDB ENTRY 1C3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100MM TRIS PH8.0, 200MM NACL, 20%(W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.37 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.43 α = 90 b = 81.01 β = 90 c = 87.83 γ = 90
Symmetry Space Group P 21 21 21
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 2009-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 45 100 0.05 96 9.5 41186
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 87.6 0.44 3710 9.3
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 PDB ENTRY 1C3D 1.7 39.78 37546 1982 100 0.17377 0.17218 0.20488 0.2003 RANDOM 24.192
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 4.865 r_scangle_it 2.998 r_scbond_it 1.952 r_mcangle_it 1.324 r_angle_refined_deg 1.231 r_mcbond_it 0.872 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 18.446 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 4.865 r_scangle_it 2.998 r_scbond_it 1.952 r_mcangle_it 1.324 r_angle_refined_deg 1.231 r_mcbond_it 0.872 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.213 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 2820 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data scaling BALBES phasing