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Crystal structure of human dUTPase complexed with Zinc.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystal condition:
0.09M 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol.
0.1M Tris (base), BICINE.
30% v/v Glycerol, PEG 4000.
(Morpheus D3)
Seeded with: 0.2M Zinc Acetate, 0.1M Sodium cacodylate, 10% v/v 2-Propanol, pH 6.5 (JCSG E7)
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.253 α = 90 b = 84.253 β = 90 c = 84.253 γ = 90
Symmetry Space Group P 21 3
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 16M 2024-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.01 48.691 100 0.998 19.5 19.4 13576
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 2.01 2.06 0.431 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.01 48.691 13553 662 99.97 0.213 0.2122 0.2147 0.2335 0.2285 RANDOM 51.567
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.173 r_dihedral_angle_6_deg 11.639 r_lrange_it 9.809 r_lrange_other 9.798 r_scangle_it 7.547 r_scangle_other 7.542 r_dihedral_angle_2_deg 6.674 r_dihedral_angle_1_deg 6.222 r_mcangle_it 6.007 r_mcangle_other 6.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.173 r_dihedral_angle_6_deg 11.639 r_lrange_it 9.809 r_lrange_other 9.798 r_scangle_it 7.547 r_scangle_other 7.542 r_dihedral_angle_2_deg 6.674 r_dihedral_angle_1_deg 6.222 r_mcangle_it 6.007 r_mcangle_other 6.003 r_scbond_it 5.044 r_scbond_other 5.039 r_mcbond_it 4.247 r_mcbond_other 4.24 r_angle_refined_deg 1.297 r_angle_other_deg 1.248 r_nbd_other 0.329 r_symmetry_nbd_other 0.214 r_symmetry_nbd_refined 0.2 r_nbd_refined 0.19 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.088 r_symmetry_metal_ion_refined 0.081 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.025 r_gen_planes_other 0.019 r_gen_planes_refined 0.01 r_bond_refined_d 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 943 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing