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Crystal structure of an NtA622L variant in complex with NADPH and Nicotinic acid N-glucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously solved structure with a different ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.05 M BIS-TRIS, 12.5% w/v Polyethylene glycol 3,350, 5 mg/ml protein, 1 mM Nicotinic acid N-glucoside
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.697 α = 110.028 b = 45.076 β = 94.801 c = 46.471 γ = 112.579
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 9M 2024-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 38.02 80.5 0.994 4 1.8 39296
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 1.5 1.53 0.89
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 38.015 39295 1935 80.509 0.201 0.1986 0.2137 0.2425 0.2495 34.361
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] -2.248 1.618 0.228 3.12 1.298 -3.347
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 37.489 r_lrange_other 35.082 r_dihedral_angle_6_deg 15.831 r_dihedral_angle_3_deg 15.528 r_mcangle_it 15.337 r_mcangle_other 15.337 r_scangle_it 12.73 r_scangle_other 12.726 r_dihedral_angle_2_deg 12.018 r_mcbond_it 11.298
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 37.489 r_lrange_other 35.082 r_dihedral_angle_6_deg 15.831 r_dihedral_angle_3_deg 15.528 r_mcangle_it 15.337 r_mcangle_other 15.337 r_scangle_it 12.73 r_scangle_other 12.726 r_dihedral_angle_2_deg 12.018 r_mcbond_it 11.298 r_mcbond_other 11.291 r_rigid_bond_restr 9.438 r_scbond_other 9.146 r_scbond_it 9.144 r_dihedral_angle_other_2_deg 7.914 r_dihedral_angle_1_deg 7.324 r_angle_refined_deg 2.263 r_angle_other_deg 1.044 r_symmetry_xyhbond_nbd_other 0.208 r_nbd_refined 0.181 r_nbtor_refined 0.152 r_symmetry_nbd_other 0.134 r_nbd_other 0.123 r_chiral_restr 0.121 r_symmetry_xyhbond_nbd_refined 0.118 r_xyhbond_nbd_refined 0.11 r_symmetry_nbd_refined 0.073 r_symmetry_nbtor_other 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing