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Crystal structure of an NtA622L variant in complex with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved structre with other ligands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 Index screen condition 78: 0.1 M Ammonium acetate, 0.05 M BIS-TRIS pH 5.5, 12.5% w/v Polyethylene glycol 3,350; 5mg/ml protein, 1mM NADP+, 1mM Trigonelline
Crystal Properties Matthews coefficient Solvent content 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.745 α = 90 b = 65.241 β = 101.603 c = 116.838 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 4M 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 ESRF MASSIF-3
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 1.65 47.504 98.4 0.074 0.101 0.068 0.996 8 3.5 112073
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 1.65 1.68 0.984 1.344 0.91 0.244 2.6
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 1.654 47.504 112050 5570 98.289 0.192 0.1911 0.1911 0.2185 0.2184 32.746
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] -0.131 -0.033 0.378 -0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.861 r_dihedral_angle_3_deg 13.554 r_dihedral_angle_other_2_deg 12.808 r_dihedral_angle_1_deg 6.739 r_lrange_it 6.402 r_lrange_other 6.36 r_dihedral_angle_2_deg 5.902 r_scangle_it 4.211 r_scangle_other 4.211 r_scbond_it 2.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.861 r_dihedral_angle_3_deg 13.554 r_dihedral_angle_other_2_deg 12.808 r_dihedral_angle_1_deg 6.739 r_lrange_it 6.402 r_lrange_other 6.36 r_dihedral_angle_2_deg 5.902 r_scangle_it 4.211 r_scangle_other 4.211 r_scbond_it 2.717 r_scbond_other 2.717 r_mcangle_it 2.704 r_mcangle_other 2.704 r_angle_refined_deg 2.076 r_mcbond_it 1.842 r_mcbond_other 1.842 r_angle_other_deg 1.01 r_nbd_refined 0.187 r_nbtor_refined 0.157 r_nbd_other 0.147 r_chiral_restr 0.135 r_symmetry_nbd_refined 0.135 r_symmetry_nbd_other 0.134 r_xyhbond_nbd_refined 0.118 r_ncsr_local_group_1 0.098 r_ncsr_local_group_3 0.091 r_ncsr_local_group_2 0.089 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.062 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7263 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction Coot model building PHASER phasing