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X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a pentylmethanesulfonamide tetramethylrhodamine ligand (TMR-S5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M MES pH 6.0, 1.0 M lithium chloride, 20% (m/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.29 α = 71.23 b = 49.93 β = 89.906 c = 78.72 γ = 67.81
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 X 16M 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999884 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 50 91.4 0.039 0.997 11.8 1.93 85890 16.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 88.6 0.432 0.77 2.51 1.99
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Y7A 1.5 43.36 1.97 85886 4295 91.52 0.1762 0.1747 0.2052 0.2173 19.92
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 6.2978 f_angle_d 1.2638 f_chiral_restr 0.0794 f_bond_d 0.0133 f_plane_restr 0.0127
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4700 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing