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Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space group.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 25% PEG 3350, 0.8M ammonium acetate, 100mM MES pH 6.5, 10mM ATP, 10mM magnesium chloride, 10mM TCEP, 2.5% PEG 400, 1mM ESO-25.
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.47 α = 90 b = 115.562 β = 104.7 c = 98.571 γ = 90
Symmetry Space Group P 1 21 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 2M 2023-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
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 1.968 73.544 96.3 0.998 7.6 3.4 135032 36.94
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 1.968 2.002 0.369
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 (Observed) 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 1.97 73.54 127152 6555 95.35 0.20113 0.19889 0.2068 0.24392 0.2476 RANDOM 52.366
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] 0.26 1.07 -2.54 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.476 r_long_range_B_other 10.198 r_long_range_B_refined 10.196 r_scangle_other 8.249 r_dihedral_angle_2_deg 7.693 r_dihedral_angle_1_deg 6.373 r_mcangle_it 6.373 r_mcangle_other 6.373 r_scbond_it 5.462 r_scbond_other 5.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.476 r_long_range_B_other 10.198 r_long_range_B_refined 10.196 r_scangle_other 8.249 r_dihedral_angle_2_deg 7.693 r_dihedral_angle_1_deg 6.373 r_mcangle_it 6.373 r_mcangle_other 6.373 r_scbond_it 5.462 r_scbond_other 5.461 r_mcbond_it 4.51 r_mcbond_other 4.51 r_angle_refined_deg 1.573 r_angle_other_deg 0.53 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 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12903 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing