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NicA2 variant N462Y/W427Y in complex with (S)-nicotine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 290 0.3 M sodium phosphate monobasic monohydrate, 1.0 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.57 52.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.486 α = 90 b = 81.486 β = 90 c = 166.304 γ = 90
Symmetry Space Group P 41 2 2
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 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 2.31 81.49 98.03 0.108 0.1185 0.04664 0.995 15.88 6 24936 47.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.393 90.07 1.094 0.6767 0.44 1.07 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TTK 2.31 81.49 1.34 24886 1998 98.03 0.201 0.1972 0.1975 0.2437 0.2432 53.46
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 6.3508 f_angle_d 0.7676 f_chiral_restr 0.0786 f_plane_restr 0.0051 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3407 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing PHENIX model building