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Adaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of recombinant NC1 hexamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Na/K phosphate, 0.2 M sodium chloride, and 26 % (w/v) PEG 1,000
Crystal Properties Matthews coefficient Solvent content 1.93 36.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.12 α = 90 b = 139.12 β = 90 c = 103.381 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 CCD MAR CCD 165 mm 2020-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 52.05 100 0.084 0.092 17.7 11.4 114327 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.533 0.589 4.3 11
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 1.75 51.69 1.34 114289 2003 99.99 0.142 0.1416 0.1416 0.1644 0.1645 23.37
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 14.5384 f_angle_d 0.8891 f_chiral_restr 0.0589 f_plane_restr 0.0071 f_bond_d 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10422 Nucleic Acid Atoms Solvent Atoms 862 Heterogen Atoms 156
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling AMoRE phasing