☰ Navigation Tabs
Structure of C3d Bound to a Fragment of FHR-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3D experimental model PDB 3ZD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.075 M HEPES [PH 7.5]
1.2 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.85 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.302 α = 90 b = 116.228 β = 90 c = 165.582 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 50 99.2 0.265 0.277 0.079 0.946 6.7 11.2 47909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 96.9 0.951 1.021 0.356 0.598 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.31 47.57 1.34 47435 2002 98.02 0.1957 0.1943 0.1938 0.2267 0.2257
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.592 f_angle_d 0.558 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6493 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing