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X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 293 PEG 8000, Sodium Acetate, Sodium Cacodylate
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.272 α = 90 b = 69.481 β = 95.82 c = 88.95 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 300 mm CCD 2016-08-22 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) Rpim 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 2.23 50 99.9 0.141 0.164 0.084 5 3.8 26164
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 2.23 2.29 100 0.616 0.722 0.374 0.777 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5UY1 2.23 44 24385 1299 97.21 0.1991 0.1975 0.2049 0.2286 0.2325 RANDOM 27.863
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] 0.51 -0.36 -0.46 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.856 r_dihedral_angle_4_deg 13.164 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 4.477 r_angle_refined_deg 0.974 r_angle_other_deg 0.73 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.856 r_dihedral_angle_4_deg 13.164 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 4.477 r_angle_refined_deg 0.974 r_angle_other_deg 0.73 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4656 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing DENZO data reduction SCALEPACK data scaling