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X-ray crystal structure of JGFN4 N76D complexed with fentanyl in monomer form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 J341, F09_10
0.1 M Buffer System 3, pH 8.5, 0.12 M Monosaccharides, 50 % v/v Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 1.66 25.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.098 α = 90 b = 26.358 β = 107.19 c = 37.458 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 16M 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 1.6 43.51 97.7 0.142 0.179 0.106 0.965 4.8 2.7 11199 26.07
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 1.6 1.63 97.9 2.525 3.091 1.756 0.445 2.7
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 1.6 43.51 1.34 11084 516 96.39 0.2357 0.2341 0.2444 0.2673 0.2844 37.33
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 14.5762 f_angle_d 0.6697 f_chiral_restr 0.0476 f_plane_restr 0.0056 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 838 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing