☰ Navigation Tabs
Nicotinic Acid N-glucoside Reductase NaGR (A622) in complex with NADP+ and Nicotinic Acid N-glucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold P52579
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.586 α = 73.2 b = 45.531 β = 79.99 c = 53.473 γ = 69.64
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER2 XE 16M 2024-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.70542 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.278 51.02 87 0.07 0.049 0.996 8 3.8 44163
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 1.278 1.544 0.614 0.614 0.592 1.6 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.28 51.02 42211 2236 51.38 0.17114 0.1691 0.1692 0.21013 0.2103 RANDOM 17.396
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] -0.06 -0.02 0.02 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.666 r_dihedral_angle_2_deg 10.807 r_dihedral_angle_1_deg 6.415 r_long_range_B_refined 5.926 r_long_range_B_other 5.69 r_scangle_other 4.069 r_mcangle_other 3.039 r_mcangle_it 3.038 r_scbond_it 2.572 r_scbond_other 2.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.666 r_dihedral_angle_2_deg 10.807 r_dihedral_angle_1_deg 6.415 r_long_range_B_refined 5.926 r_long_range_B_other 5.69 r_scangle_other 4.069 r_mcangle_other 3.039 r_mcangle_it 3.038 r_scbond_it 2.572 r_scbond_other 2.571 r_mcbond_it 1.965 r_mcbond_other 1.965 r_angle_refined_deg 1.88 r_angle_other_deg 0.616 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2406 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing