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Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 co-crystallisation with diphosphate AT-9052F compound.
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.22 α = 90 b = 121.06 β = 107.135 c = 70.76 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 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980105 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.553 48.668 97.2 0.037 0.997 11.4 3.9 121746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.553 1.58 93.9 0.321 0.723 2.1 3.2
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 1.553 48.668 121745 6018 97.161 0.172 0.1701 0.1705 0.1995 0.1996 20.57
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] -0.709 -0.046 -0.395 0.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.985 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_2_deg 9.35 r_scangle_it 8.09 r_scangle_other 8.09 r_lrange_it 7.646 r_lrange_other 7.636 r_scbond_it 6.639 r_scbond_other 6.639 r_dihedral_angle_1_deg 6.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.985 r_dihedral_angle_3_deg 13.484 r_dihedral_angle_2_deg 9.35 r_scangle_it 8.09 r_scangle_other 8.09 r_lrange_it 7.646 r_lrange_other 7.636 r_scbond_it 6.639 r_scbond_other 6.639 r_dihedral_angle_1_deg 6.484 r_mcangle_other 3.253 r_mcangle_it 3.252 r_mcbond_it 2.639 r_mcbond_other 2.638 r_angle_refined_deg 1.738 r_dihedral_angle_other_2_deg 0.806 r_angle_other_deg 0.59 r_nbd_refined 0.227 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.15 r_nbd_other 0.126 r_chiral_restr 0.1 r_ncsr_local_group_2 0.083 r_ncsr_local_group_5 0.078 r_ncsr_local_group_3 0.077 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_1 0.075 r_ncsr_local_group_4 0.072 r_ncsr_local_group_6 0.064 r_ncsr_local_group_15 0.064 r_ncsr_local_group_11 0.061 r_ncsr_local_group_12 0.061 r_ncsr_local_group_8 0.06 r_ncsr_local_group_9 0.06 r_ncsr_local_group_7 0.058 r_ncsr_local_group_10 0.056 r_ncsr_local_group_14 0.056 r_ncsr_local_group_13 0.05 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7284 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing