☰ Navigation Tabs
X-Ray crystal structure of a photoswitchable HaloTag bound to JF635
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 crystallization condition: (0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium nitrate, 20% (w/v) PEG3350, 10% (v/v) ethylene glycol); mixed 1:1 with protein in buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl)
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.737 α = 90 b = 78.017 β = 103.92 c = 81.807 γ = 90
Symmetry Space Group C 1 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 EIGER2 S 9M KB mirror 2024-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 2.4 70.36 99.7 0.294 0.318 0.119 0.985 5.1 7 40131
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 2.4 2.49 99.7 1.702 1.835 0.682 0.58 7.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 70.36 1.34 40102 2039 99.56 0.1881 0.1855 0.189 0.2354 0.2353 aimless random 5%
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 15.927 f_angle_d 1.012 f_chiral_restr 0.056 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6992 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 230
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement