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Complement component C2a, the catalytic fragment of C3- and C5-convertase of human complement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ODQ PDB ENTRY 2ODQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 20% PEG 10000, 0.1M HEPES, 0.3M glycyl-glycyl-glycine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.82 56.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.398 α = 90 b = 83.819 β = 92.1 c = 75.243 γ = 90
Symmetry Space Group P 1 21 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 MAR CCD 225 mm 2006-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97969 APS 22-BM
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 1.9 50.48 98 0.04 31.7 49897
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 1.9 1.97 91.3 0.17 7.1
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 2ODQ 1.9 30 48766 2475 97.76 0.209 0.207 0.2058 0.25 0.2497 RANDOM 24.319
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] 0.61 0.98 0.25 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.64 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_1_deg 6.104 r_scangle_it 4.618 r_scbond_it 3.104 r_mcangle_it 1.813 r_angle_refined_deg 1.637 r_mcbond_it 1.491 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.64 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_1_deg 6.104 r_scangle_it 4.618 r_scbond_it 3.104 r_mcangle_it 1.813 r_angle_refined_deg 1.637 r_mcbond_it 1.491 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.116 r_metal_ion_refined 0.042 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3873 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing