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Bacteriophage T5 dUTPase mutant with loop deletion (30-35 aa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 0.085 M HEPES sodium, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.726 α = 90 b = 88.726 β = 90 c = 99.999 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 120 PIXEL RIGAKU HyPix-6000HE 2023-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 23 99.1 0.094 0.998 13.4 9 26147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.51 0.954 3.2
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 2.1 20.001 24792 1160 94.905 0.223 0.2206 0.2255 0.2641 0.2695 31.508
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] -0.232 -0.116 -0.232 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.02 r_dihedral_angle_6_deg 16.549 r_dihedral_angle_1_deg 6.694 r_dihedral_angle_2_deg 6.668 r_lrange_it 4.384 r_lrange_other 4.302 r_scangle_it 2.656 r_scangle_other 2.466 r_mcangle_it 1.938 r_mcangle_other 1.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.02 r_dihedral_angle_6_deg 16.549 r_dihedral_angle_1_deg 6.694 r_dihedral_angle_2_deg 6.668 r_lrange_it 4.384 r_lrange_other 4.302 r_scangle_it 2.656 r_scangle_other 2.466 r_mcangle_it 1.938 r_mcangle_other 1.938 r_scbond_it 1.72 r_scbond_other 1.561 r_angle_refined_deg 1.342 r_mcbond_it 1.21 r_mcbond_other 1.21 r_angle_other_deg 0.461 r_nbd_other 0.221 r_symmetry_nbd_other 0.205 r_nbd_refined 0.193 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.068 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3045 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing