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Ground-state model of NUDT5 and corresponding apo datasets for PanDDA analysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GRU 6GRU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.074 α = 79.44 b = 59.679 β = 81.82 c = 80.321 γ = 75.93
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 PILATUS 6M 2018-07-29 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 1.000 Diamond I04-1
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 1.58 47.32 95.6 0.032 0.045 0.032 0.997 9.8 1.7 113271
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 1.58 1.62 93.1 0.338 0.478 0.338 0.813 1.5 8144
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 FOURIER SYNTHESIS THROUGHOUT 6GRU 1.58 78.54 107537 5723 95.5 0.221 0.2194 0.3285 0.25 0.3309 RANDOM 30.765
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] 2.23 0.86 0.53 -0.42 0.65 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.291 r_dihedral_angle_3_deg 13.442 r_dihedral_angle_4_deg 12.989 r_dihedral_angle_1_deg 6.855 r_mcangle_it 4.058 r_mcbond_it 3.062 r_mcbond_other 3.044 r_angle_refined_deg 1.997 r_angle_other_deg 1.039 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.291 r_dihedral_angle_3_deg 13.442 r_dihedral_angle_4_deg 12.989 r_dihedral_angle_1_deg 6.855 r_mcangle_it 4.058 r_mcbond_it 3.062 r_mcbond_other 3.044 r_angle_refined_deg 1.997 r_angle_other_deg 1.039 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5700 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing