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Crystal structure of Efb-C / C3d Complex
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 VAPOR DIFFUSION, HANGING DROP 7.4 293 60% Tacsimate pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.11 60.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.939 α = 90 b = 90.939 β = 90 c = 122.242 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 93 CCD MARMOSAIC 300 mm CCD mirrors 2005-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.9184 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 99 0.11 0.092 9 4.9 50259 49761
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 2.2 2.28 92.4 92.4 0.532 1.8 3.5
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 (All) 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 2.2 50 49718 2519 98.82 0.184 0.181 0.231 0.2256 RANDOM 43.528
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] -0.97 -0.97 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 18.533 r_dihedral_angle_1_deg 6.477 r_scangle_it 4.37 r_scbond_it 2.978 r_angle_refined_deg 1.877 r_mcangle_it 1.867 r_mcbond_it 1.164 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 18.533 r_dihedral_angle_1_deg 6.477 r_scangle_it 4.37 r_scbond_it 2.978 r_angle_refined_deg 1.877 r_mcangle_it 1.867 r_mcbond_it 1.164 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.129 r_symmetry_hbond_refined 0.095 r_bond_refined_d 0.024 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction