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Crystal structure of NUDT14 complexed with novel compound AMNUDT14-003 in spacegroup P1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 Hampton Crystal Screen condition A09
30% PEG4000
0.2M ammonium acetate
0.1M citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.886 α = 89.955 b = 85.392 β = 89.998 c = 106.742 γ = 78.77
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 XE 16M 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.162 106.742 85.2 0.981 3.2 3.6 12794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.162 3.666 0.819
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 3.162 106.742 12794 644 40.137 0.214 0.211 0.211 0.2652 0.2653 47.576
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] -1.703 -0.791 0.286 -0.478 0.034 1.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.084 r_dihedral_angle_6_deg 12.28 r_lrange_it 12.135 r_dihedral_angle_2_deg 8.104 r_dihedral_angle_1_deg 7.036 r_mcangle_it 6.095 r_scangle_it 5.76 r_mcbond_it 3.431 r_scbond_it 3.254 r_angle_refined_deg 1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.084 r_dihedral_angle_6_deg 12.28 r_lrange_it 12.135 r_dihedral_angle_2_deg 8.104 r_dihedral_angle_1_deg 7.036 r_mcangle_it 6.095 r_scangle_it 5.76 r_mcbond_it 3.431 r_scbond_it 3.254 r_angle_refined_deg 1.357 r_symmetry_xyhbond_nbd_refined 0.426 r_symmetry_nbd_refined 0.409 r_nbtor_refined 0.308 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.096 r_ncsr_local_group_7 0.093 r_ncsr_local_group_22 0.087 r_ncsr_local_group_13 0.085 r_ncsr_local_group_25 0.084 r_ncsr_local_group_27 0.084 r_ncsr_local_group_18 0.081 r_ncsr_local_group_9 0.078 r_ncsr_local_group_28 0.078 r_ncsr_local_group_3 0.075 r_ncsr_local_group_5 0.075 r_ncsr_local_group_19 0.074 r_ncsr_local_group_21 0.074 r_ncsr_local_group_20 0.073 r_ncsr_local_group_24 0.073 r_ncsr_local_group_10 0.072 r_ncsr_local_group_15 0.071 r_ncsr_local_group_4 0.07 r_ncsr_local_group_26 0.068 r_ncsr_local_group_23 0.067 r_ncsr_local_group_14 0.064 r_ncsr_local_group_11 0.063 r_ncsr_local_group_6 0.061 r_ncsr_local_group_16 0.059 r_ncsr_local_group_1 0.056 r_ncsr_local_group_12 0.054 r_ncsr_local_group_2 0.051 r_ncsr_local_group_8 0.047 r_ncsr_local_group_17 0.045 r_gen_planes_refined 0.006 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12850 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing