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Crystal structure of an NtA622L variant in complex with NADPH and Trigonelline
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 6.5 291 5 mg/ml Protein, 1 mM Trigonelline, 0.5 mM NADPH, 0.1 M Sodium chloride, 0.05 M BIS-TRIS, 12.5% PEG 3350,
500x diluted seed stock
Crystal Properties Matthews coefficient Solvent content 2.34 47.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.227 α = 90 b = 64.917 β = 101.513 c = 115.352 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2024-04-18 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) 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 2.6 64.92 97.8 0.267 0.377 0.266 0.615 5.9 3.3 29126
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 2.6 2.72 1.026 1.449 1.023 0.436 3.5
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 2.6 56.293 29110 1471 97.609 0.209 0.2062 0.2078 0.2678 0.2699 60.844
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] -2.908 1.836 1.061 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.261 r_dihedral_angle_2_deg 16.29 r_dihedral_angle_6_deg 15.411 r_dihedral_angle_1_deg 7.772 r_dihedral_angle_other_2_deg 7.59 r_lrange_it 7.512 r_lrange_other 7.512 r_scangle_it 3.316 r_scangle_other 3.316 r_mcangle_it 2.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.261 r_dihedral_angle_2_deg 16.29 r_dihedral_angle_6_deg 15.411 r_dihedral_angle_1_deg 7.772 r_dihedral_angle_other_2_deg 7.59 r_lrange_it 7.512 r_lrange_other 7.512 r_scangle_it 3.316 r_scangle_other 3.316 r_mcangle_it 2.976 r_mcangle_other 2.976 r_angle_refined_deg 2.671 r_scbond_it 2.044 r_scbond_other 2.043 r_mcbond_it 1.822 r_mcbond_other 1.822 r_angle_other_deg 0.954 r_symmetry_xyhbond_nbd_refined 0.322 r_symmetry_nbd_refined 0.272 r_nbd_refined 0.21 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.175 r_nbd_other 0.174 r_symmetry_nbd_other 0.17 r_chiral_restr 0.13 r_ncsr_local_group_1 0.126 r_ncsr_local_group_3 0.123 r_ncsr_local_group_2 0.117 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7251 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing Coot model building