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Structure of J paramyxovirus virus receptor binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Crystals grew in 0.1 M carboxylic acid, 0.1 M tris/bicine pH 8.5, 6% sucrose, 0.2 M ammonium sulphate, 37.5% Morpheus (Molecular dimensions) precipitant mix 4, consisting of 25% v/v 2-methyl-2,4-pentanediol (MPD), 25% w/v PEG 1000 (P1k) and 25% w/v polyethylene glycol 3350 (PEG 3350).
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.24 α = 90 b = 164.24 β = 90 c = 112.47 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 PIXEL DECTRIS PILATUS 6M-F 2017-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 2.2 60.11 100 0.18 0.19 0.06 0.99 9.6 10.2 87311
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 2.2 2.24 2.34 2.46 0.76 0.48 1.3
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 2.2 46.4 1.33 87311 4448 99.94 0.1903 0.1893 0.1898 0.2071 0.2072
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 13.607 f_angle_d 0.632 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6764 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing