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Crystal structure of an NtA622L variant in complex with NADP+ and Nicotinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved structure with different ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.05 M Tris pH 8.5, 1.0 M Ammonium sulfate, 5 mM Nicotinic acid, 5 mg/ml protein (Index HT screen condition 6)
Crystal Properties Matthews coefficient Solvent content 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.026 α = 90 b = 63.353 β = 105.679 c = 61.088 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 EIGER2 X 16M 2023-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03272 PETRA III, DESY P11
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 1.68 43.104 98.6 0.178 0.212 0.113 0.993 7.2 6.7 34175
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 1.68 1.7 1.685 2.006 1.073 0.536 6.6
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 1.68 43.104 33939 1763 98.517 0.182 0.1795 0.1797 0.22 0.2207 27.234
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] 1.571 0.367 -1.261 -0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 19.349 r_dihedral_angle_6_deg 15.04 r_dihedral_angle_3_deg 13.449 r_lrange_it 8.732 r_lrange_other 8.709 r_dihedral_angle_2_deg 8.496 r_dihedral_angle_1_deg 7.258 r_scangle_it 7.058 r_scangle_other 7.056 r_scbond_other 4.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 19.349 r_dihedral_angle_6_deg 15.04 r_dihedral_angle_3_deg 13.449 r_lrange_it 8.732 r_lrange_other 8.709 r_dihedral_angle_2_deg 8.496 r_dihedral_angle_1_deg 7.258 r_scangle_it 7.058 r_scangle_other 7.056 r_scbond_other 4.641 r_scbond_it 4.638 r_mcangle_it 4.33 r_mcangle_other 4.33 r_mcbond_it 3.009 r_mcbond_other 3.001 r_angle_refined_deg 2.186 r_angle_other_deg 0.857 r_nbd_refined 0.209 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.166 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.128 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Coot model building MOLREP phasing