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Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement fragment C3d
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1C3D 1.7 44.59 37547 1982 100 0.17053 0.16878 0.1673 0.20471 0.2021 RANDOM 24.359
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] 0.28 -0.24 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.599 r_dihedral_angle_4_deg 21.419 r_dihedral_angle_3_deg 12.96 r_dihedral_angle_1_deg 4.809 r_scangle_it 2.84 r_scbond_it 1.862 r_mcangle_it 1.316 r_angle_refined_deg 1.208 r_mcbond_it 0.881 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.599 r_dihedral_angle_4_deg 21.419 r_dihedral_angle_3_deg 12.96 r_dihedral_angle_1_deg 4.809 r_scangle_it 2.84 r_scbond_it 1.862 r_mcangle_it 1.316 r_angle_refined_deg 1.208 r_mcbond_it 0.881 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.149 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 2828 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data scaling BALBES phasing