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Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.3 293 20% (w/v) PEG 3350
0.2M potassium citrate tribasic monohydrate
0.02M CdCl(2)
0.02M m7GTP
Crystal Properties Matthews coefficient Solvent content 3.53 65.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.859 α = 90 b = 229.859 β = 90 c = 159.012 γ = 120
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 Toroidal mirror 2019-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.0077 SOLEIL PROXIMA 2
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 2.9 114.93 95.8 0.117 0.124 0.039 0.998 11.6 10.1 21142
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 2.9 3.2 88.1 1.47 1.56 0.51 0.633 1.8 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6O3P 2.92 114.93 21142 1062 60.2 0.233 0.232 0.2459 0.26 0.285 RANDOM 94.16
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] -1.8037 -1.8037 3.6075
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.16 t_omega_torsion 2.1 t_angle_deg 0.9 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.16 t_omega_torsion 2.1 t_angle_deg 0.9 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7556 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 207
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction Coot model building PHASER phasing pointless data scaling XDS data reduction autoPROC data scaling STARANISO data scaling MxCuBE data collection