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C3b in complex with a C3b specific Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ICF PDB entry 2ICF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C
from 4 ml hanging drops, consisting of a 1:1 ratio of protein
solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to
mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0),
suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.93 58.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.436 α = 90 b = 180.417 β = 115.73 c = 154.584 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315 mirrors 2007-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.05 50 100 0.0135 3.7 101495 101590
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.16 100 0.667 2.1 4.5 10108
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2ICF 3.1 20 96423 96819 4825 99.99 0.2178 0.2178 0.21437 0.2254 0.2822 0.2874 RANDOM 35.199
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] 0.78 0.23 -1.05 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_3_deg 17.418 r_dihedral_angle_4_deg 15.627 r_dihedral_angle_1_deg 6.371 r_mcangle_it 3.208 r_scangle_it 2.177 r_mcbond_it 1.913 r_scbond_it 1.36 r_angle_refined_deg 1.025 r_angle_other_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_3_deg 17.418 r_dihedral_angle_4_deg 15.627 r_dihedral_angle_1_deg 6.371 r_mcangle_it 3.208 r_scangle_it 2.177 r_mcbond_it 1.913 r_scbond_it 1.36 r_angle_refined_deg 1.025 r_angle_other_deg 0.792 r_metal_ion_refined 0.234 r_mcbond_other 0.198 r_nbd_refined 0.185 r_nbd_other 0.18 r_nbtor_refined 0.174 r_symmetry_vdw_other 0.155 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.08 r_chiral_restr 0.061 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31006 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling