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Crystal structure of human USP25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG 3350, sodium fluoride
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.806 α = 90 b = 140.806 β = 90 c = 190.156 γ = 90
Symmetry Space Group I 4 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 100 PIXEL DECTRIS PILATUS 300K 2016-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9791 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.283 95.08 99.5 0.068 0.078 0.041 16.3 6.5 14883
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.283 3.294 97.7 0.984 1.181 0.626 2.3 6.4
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 SAD THROUGHOUT 3.283 95.08 14150 722 99.32 0.20586 0.20235 0.2048 0.27514 0.2698 RANDOM 146.785
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] 4.85 4.85 -9.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_long_range_B_other 21.047 r_long_range_B_refined 21.044 r_dihedral_angle_3_deg 20.002 r_scangle_other 16.102 r_mcangle_it 15.95 r_mcangle_other 15.947 r_dihedral_angle_4_deg 14.271 r_mcbond_it 10.533 r_mcbond_other 10.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.694 r_long_range_B_other 21.047 r_long_range_B_refined 21.044 r_dihedral_angle_3_deg 20.002 r_scangle_other 16.102 r_mcangle_it 15.95 r_mcangle_other 15.947 r_dihedral_angle_4_deg 14.271 r_mcbond_it 10.533 r_mcbond_other 10.514 r_scbond_it 10.407 r_scbond_other 10.406 r_dihedral_angle_1_deg 8.302 r_angle_refined_deg 1.524 r_angle_other_deg 1.023 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3963 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing