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Human Complement Membrane Attack Proteins Share a Common Fold with Bacterial Cytolysins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Lower resolution model solved by SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 6% PEG 20,000, 0.1 M citric acid, 0.025 M Mg(NO3)2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.553 α = 90 b = 126.087 β = 90 c = 51.887 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9565 APS 21-ID-D
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 2.15 50 93.2 0.048 0.048 33.4 4 32462 32462 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.24 84.2 0.4 0.315 2.6 3.1 2876
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 Lower resolution model solved by SAD 2.15 34 30735 30735 1616 91.87 0.20827 0.20827 0.20563 0.2816 0.26086 0.3339 RANDOM 45.718
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] 0.11 -1.59 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.382 r_dihedral_angle_4_deg 19.409 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_1_deg 7.395 r_scangle_it 3.613 r_scbond_it 2.323 r_mcangle_it 1.705 r_angle_refined_deg 1.63 r_mcbond_it 1.022 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.382 r_dihedral_angle_4_deg 19.409 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_1_deg 7.395 r_scangle_it 3.613 r_scbond_it 2.323 r_mcangle_it 1.705 r_angle_refined_deg 1.63 r_mcbond_it 1.022 r_angle_other_deg 0.886 r_symmetry_vdw_other 0.256 r_mcbond_other 0.227 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.205 r_nbd_other 0.198 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.107 r_nbtor_other 0.091 r_symmetry_hbond_refined 0.081 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined 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 3844 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXD phasing SHELXE model building ARP/wARP model building RESOLVE phasing O model building CCP4 phasing MOLREP phasing Coot model building