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Crystal structure of complement C5 in complex with SKY59
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BBJ 1BBJ, 3CU7 experimental model PDB 3CU7 1BBJ, 3CU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M magnesium formate dehydrate, 15.0% w/v polyethylene glycol 3350, 20% v/v glycerol as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.79 α = 89.18 b = 55.1 β = 86.24 c = 127.76 γ = 78.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RAYONIX MX-225 2015-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
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 2.11 42.49 92.1 0.072 7.9 2 56154
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 2.11 2.16 95.8 0.317 1.8 2
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 1BBJ, 3CU7 2.11 25 53398 2724 92.04 0.2478 0.2459 0.2482 0.2853 0.2881 RANDOM 38.604
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] 1.72 0.86 1.39 -0.39 1.52 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.229 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_4_deg 12.572 r_dihedral_angle_1_deg 4.827 r_mcangle_it 1.332 r_angle_refined_deg 1.062 r_mcbond_it 0.717 r_scbond_it 0.46 r_chiral_restr 0.06 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.229 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_4_deg 12.572 r_dihedral_angle_1_deg 4.827 r_mcangle_it 1.332 r_angle_refined_deg 1.062 r_mcbond_it 0.717 r_scbond_it 0.46 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7895 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms
Software Software Software Name Purpose XDS data processing Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction