☰ Navigation Tabs
The Crystal Structure of C2b, a Fragment of Complement Component C2 produced during C3-convertase Formation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OK5 PDB ENTRY 2OK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 18% PEG 3350, 0.22M Sodium Chloride, 0.02M Betaine Hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.06 α = 90 b = 60.06 β = 90 c = 61.687 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 40 100 0.033 21 4.36 23095
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) 1.8 1.86 100 0.237 5.1 4.15
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 2OK5 1.8 21.52 21882 1182 99.9 0.21552 0.2142 0.2141 0.23963 0.2394 RANDOM 23.257
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] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.163 r_dihedral_angle_4_deg 16.708 r_dihedral_angle_3_deg 12.198 r_dihedral_angle_1_deg 6.3 r_scangle_it 3.341 r_scbond_it 2.07 r_angle_refined_deg 1.243 r_mcangle_it 1.157 r_mcbond_it 0.813 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.163 r_dihedral_angle_4_deg 16.708 r_dihedral_angle_3_deg 12.198 r_dihedral_angle_1_deg 6.3 r_scangle_it 3.341 r_scbond_it 2.07 r_angle_refined_deg 1.243 r_mcangle_it 1.157 r_mcbond_it 0.813 r_nbtor_refined 0.301 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1415 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms
Software Software Software Name Purpose CNS refinement REFMAC refinement d*TREK data reduction d*TREK data scaling CNS phasing