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Human SMUG1 in complex with DNA
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 diammonium hydrogen citrate pH 4.9, 60% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.072 α = 90 b = 84.366 β = 113.403 c = 88.259 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2023-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6702 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 2.1 72.045 100 0.994 5.9 12.7 56982
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 2.1 2.16 0.328
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 72.045 47057 2374 79.681 0.209 0.2066 0.2058 0.2534 0.253 39.311
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] -0.331 0.166 0.021 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.575 r_dihedral_angle_3_deg 13.748 r_dihedral_angle_2_deg 7.696 r_dihedral_angle_1_deg 7.169 r_lrange_it 7.161 r_lrange_other 7.157 r_scangle_it 3.93 r_scangle_other 3.93 r_mcangle_it 2.526 r_mcangle_other 2.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.575 r_dihedral_angle_3_deg 13.748 r_dihedral_angle_2_deg 7.696 r_dihedral_angle_1_deg 7.169 r_lrange_it 7.161 r_lrange_other 7.157 r_scangle_it 3.93 r_scangle_other 3.93 r_mcangle_it 2.526 r_mcangle_other 2.526 r_scbond_it 2.451 r_scbond_other 2.451 r_mcbond_it 1.454 r_mcbond_other 1.453 r_angle_refined_deg 1.425 r_angle_other_deg 0.426 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_other 0.226 r_symmetry_nbd_other 0.217 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.065 r_gen_planes_other 0.006 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_dihedral_angle_other_2_deg
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7732 Nucleic Acid Atoms 970 Solvent Atoms 242 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing