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Structure of NUDT15 in complex with Geranyl monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LPG 5LPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 30 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.642 α = 90 b = 48.269 β = 90 c = 135.197 γ = 90
Symmetry Space Group P 21 21 21
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 2018-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
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 1.7 46.64 99.7 0.998 17.8 11.3 34417
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 1.7 1.73 0.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LPG 1.7 45.5 34343 1722 99.64 0.186 0.1841 0.1969 0.2263 0.228 27.836
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] -0.551 2.346 -1.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.385 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 15.891 r_lrange_it 7.444 r_lrange_other 7.434 r_dihedral_angle_1_deg 7.03 r_scangle_it 5.837 r_scangle_other 5.835 r_scbond_it 3.795 r_scbond_other 3.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.385 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 15.891 r_lrange_it 7.444 r_lrange_other 7.434 r_dihedral_angle_1_deg 7.03 r_scangle_it 5.837 r_scangle_other 5.835 r_scbond_it 3.795 r_scbond_other 3.788 r_mcangle_other 3.368 r_mcangle_it 3.366 r_mcbond_it 2.523 r_mcbond_other 2.517 r_angle_refined_deg 1.715 r_angle_other_deg 1.432 r_nbd_refined 0.216 r_symmetry_nbd_other 0.187 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.156 r_symmetry_nbd_refined 0.125 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.081 r_metal_ion_refined 0.06 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2471 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing