☰ Navigation Tabs
Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 5% (w/v) PEG 20000, 25% (w/v) trimethylpropane, 0.1 M N,N-bis(2-hydroxyethyl)-2-amino ethanesulfonic acid (BES)/triethanolamine pH 7.5, 1% (w/v) non-detergent sulfobetaine (NDSB) 195, 0.5 mM YCl3, 0.5 mM ErCl3, 0.5 mM TbCl3, 0.5 mM YbCl3
Crystal Properties Matthews coefficient Solvent content 5.85 79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.35 α = 90 b = 108.35 β = 90 c = 255.07 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M 2018-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29
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 4.2 88.06 98.5 0.2067 0.2244 0.0849 0.994 4.42 6.4 13155 204.6
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 4.2 4.524 99.2 2.457 2.649 0.9651 0.712 0.81 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AlphaFold2 models 4.2 88.06 1.35 13085 652 98.58 0.3305 0.3285 0.3344 0.3677 0.3714 286.48
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 10.9609 f_angle_d 0.6287 f_chiral_restr 0.0489 f_plane_restr 0.0056 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4613 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building CNS refinement PHENIX refinement