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Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010
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 mixing 1:1 ration with precipitant solution composed of:
-50mM Tris-HCl pH8.4
-12% PEG3350
-16% glycerol
Crystal Properties Matthews coefficient Solvent content 2.12 41.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.19 α = 90 b = 120.313 β = 110.154 c = 71.918 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 2023-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801073689120102 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 1.9 49.68 98.89 0.0552 0.996 8.61 7.1 67263
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 1.9 1.968 98 0.3295 0.793 2.57 7.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 49.68 67261 3342 98.902 0.174 0.1724 0.213 0.2182 24.719
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] -0.471 -0.662 0.22 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.857 r_dihedral_angle_2_deg 14.869 r_dihedral_angle_3_deg 14.821 r_lrange_it 8.374 r_lrange_other 8.362 r_scangle_it 8.248 r_scangle_other 8.247 r_dihedral_angle_1_deg 6.536 r_scbond_it 5.694 r_scbond_other 5.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.857 r_dihedral_angle_2_deg 14.869 r_dihedral_angle_3_deg 14.821 r_lrange_it 8.374 r_lrange_other 8.362 r_scangle_it 8.248 r_scangle_other 8.247 r_dihedral_angle_1_deg 6.536 r_scbond_it 5.694 r_scbond_other 5.694 r_mcangle_it 3.578 r_mcangle_other 3.578 r_mcbond_it 2.881 r_mcbond_other 2.881 r_angle_refined_deg 2.05 r_angle_other_deg 0.699 r_symmetry_nbd_refined 0.453 r_nbd_other 0.336 r_symmetry_xyhbond_nbd_refined 0.321 r_symmetry_xyhbond_nbd_other 0.243 r_nbd_refined 0.231 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_10 0.075 r_ncsr_local_group_12 0.074 r_ncsr_local_group_13 0.073 r_ncsr_local_group_6 0.071 r_ncsr_local_group_14 0.071 r_ncsr_local_group_5 0.07 r_ncsr_local_group_9 0.069 r_ncsr_local_group_3 0.067 r_ncsr_local_group_4 0.067 r_ncsr_local_group_7 0.067 r_ncsr_local_group_2 0.066 r_ncsr_local_group_8 0.064 r_ncsr_local_group_1 0.063 r_ncsr_local_group_11 0.058 r_ncsr_local_group_15 0.055 r_dihedral_angle_other_2_deg 0.026 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 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 402 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing