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dUTPase from human in complex with Stl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H49 experimental model PDB 1Q5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 1.6M ammonium sulphate and 1M lithium sulphate.
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.72 α = 90 b = 81.797 β = 90 c = 198.398 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 80 PIXEL DECTRIS EIGER2 X 9M 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99186 Diamond I24
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 1.944 99.2 98.48 0.999 18.9 12.9 92354
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 1.944 1.995 0.897
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6H49, 1Q5U 1.944 99.199 92311 4665 98.495 0.217 0.21659 0.21424 0.26191 0.2544 48.965
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] 4.944 -1.866 -3.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 17.444 r_lrange_other 7.786 r_lrange_it 7.785 r_dihedral_angle_1_deg 6.718 r_mcangle_it 5.641 r_mcangle_other 5.641 r_scangle_it 5.589 r_scangle_other 5.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.022 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 17.444 r_lrange_other 7.786 r_lrange_it 7.785 r_dihedral_angle_1_deg 6.718 r_mcangle_it 5.641 r_mcangle_other 5.641 r_scangle_it 5.589 r_scangle_other 5.589 r_scbond_it 3.932 r_scbond_other 3.932 r_mcbond_it 3.921 r_mcbond_other 3.921 r_angle_refined_deg 1.485 r_angle_other_deg 1.338 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_other 0.21 r_nbd_refined 0.198 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.078 r_chiral_restr 0.068 r_xyhbond_nbd_other 0.034 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6555 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing