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Human SMUG1 in complex with 5-fluorouracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Buffer System 3 pH 8.4, 80 % (v/v) P500MME_P20K, 0.12 M Alcohols Mix (Morpheus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.558 α = 90 b = 59.975 β = 90 c = 91.293 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 EIGER2 X 16M 2023-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.899 50.126 99.2 0.993 7.5 12.4 21518
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 1.899 1.932 0.708
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 1.899 50.126 21468 1104 98.899 0.193 0.1905 0.1905 0.2333 0.233 28.738
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] -0.196 0.74 -0.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.053 r_dihedral_angle_3_deg 11.673 r_dihedral_angle_2_deg 10.03 r_lrange_other 6.46 r_lrange_it 6.435 r_dihedral_angle_1_deg 6.172 r_scangle_it 5.011 r_scangle_other 5.01 r_scbond_it 3.249 r_scbond_other 3.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.053 r_dihedral_angle_3_deg 11.673 r_dihedral_angle_2_deg 10.03 r_lrange_other 6.46 r_lrange_it 6.435 r_dihedral_angle_1_deg 6.172 r_scangle_it 5.011 r_scangle_other 5.01 r_scbond_it 3.249 r_scbond_other 3.248 r_mcangle_it 2.979 r_mcangle_other 2.978 r_mcbond_it 2.082 r_mcbond_other 2.067 r_angle_refined_deg 1.63 r_angle_other_deg 0.52 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.182 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 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 1927 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction Aimless data scaling PHASER phasing