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Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Protein: 20mg/mL
Precipitant condition: 17% PEG 6K, 20mM NaF, 1mM ZnCl, 0.1M Hepes pH 7, 10 mM Na6[(PO3)6]
Ratio: 1:1
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.942 α = 90 b = 59.942 β = 90 c = 83.078 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M 2022-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 1.54 51.91 84.4 0.01 0.99 25.7 12.7 19582 29.7
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 1.54 1.63 0.46 0.59 1.1
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 1.541 51.91 19582 918 75.033 0.201 0.1989 0.2068 0.2339 0.2418 32.669
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] -0.026 -0.013 -0.026 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.936 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_2_deg 10.835 r_lrange_it 9.346 r_lrange_other 9.301 r_scangle_it 7.402 r_scangle_other 7.133 r_dihedral_angle_1_deg 7.125 r_scbond_it 4.833 r_scbond_other 4.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.936 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_2_deg 10.835 r_lrange_it 9.346 r_lrange_other 9.301 r_scangle_it 7.402 r_scangle_other 7.133 r_dihedral_angle_1_deg 7.125 r_scbond_it 4.833 r_scbond_other 4.577 r_mcangle_other 4.44 r_mcangle_it 4.438 r_mcbond_it 3.233 r_mcbond_other 3.217 r_angle_refined_deg 1.808 r_angle_other_deg 0.611 r_xyhbond_nbd_refined 0.221 r_nbd_other 0.219 r_nbd_refined 0.21 r_symmetry_nbd_other 0.199 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.16 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1025 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 21
Software Software Software Name Purpose autoPROC data processing REFMAC refinement Coot model building MOLREP phasing autoPROC data reduction autoPROC data scaling