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Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (P1 space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PVE PDB entry 6PVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES, pH 7.0, 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.676 α = 82.941 b = 62.031 β = 81.924 c = 106.975 γ = 68.522
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 EIGER X 16M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.08 50 91 0.177 0.092 0.975 8.5 3.6 59068 23.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.15 84 0.583 3.4
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 PDB entry 6PVE 2.08 41.26 1.96 59041 1990 91.15 0.1951 0.1936 0.194 0.2396 0.2408 27.51
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 15.1049 f_angle_d 0.7016 f_chiral_restr 0.0466 f_plane_restr 0.0053 f_bond_d 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7994 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 166
Software Software Software Name Purpose JBluIce-EPICS data collection HKL-2000 data reduction Coot model building PHASER phasing PHENIX refinement