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Crystal structure of Usp10 catalytic domain (apo state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium sulfate, 20% PEG 3350, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.79 α = 90 b = 107.79 β = 90 c = 131.15 γ = 120
Symmetry Space Group P 63 2 2
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 XE 16M 2024-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.8 76.05 100 1 23.3 40 42256
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 1.8 9 0.738
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 1.8 50.01 40122 2101 99.94 0.17388 0.17191 0.1725 0.21289 0.2129 RANDOM 45.571
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] 0.72 0.36 0.72 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.361 r_long_range_B_refined 11.491 r_long_range_B_other 11.465 r_dihedral_angle_2_deg 9.549 r_scangle_other 7.971 r_dihedral_angle_1_deg 6.332 r_mcangle_other 5.492 r_mcangle_it 5.482 r_scbond_it 5.217 r_scbond_other 5.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.361 r_long_range_B_refined 11.491 r_long_range_B_other 11.465 r_dihedral_angle_2_deg 9.549 r_scangle_other 7.971 r_dihedral_angle_1_deg 6.332 r_mcangle_other 5.492 r_mcangle_it 5.482 r_scbond_it 5.217 r_scbond_other 5.179 r_mcbond_it 3.717 r_mcbond_other 3.715 r_angle_refined_deg 1.69 r_angle_other_deg 1.011 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 2673 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction