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Crystal structure of USP7 ubiquitin-like domains in extended conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 sodium chloride, TRIS-HCl, 2-mercaptoethanol, betaine hydrochloride
Crystal Properties Matthews coefficient Solvent content 4.09 69.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.99 α = 90 b = 164.99 β = 90 c = 110.12 γ = 90
Symmetry Space Group P 42 21 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 CCD MARMOSAIC 300 mm CCD 2012-10-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97849 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.4 42.3 99.7 24.3 9.5 21462
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 THROUGHOUT 3.4 30 20318 1138 99.87 0.2429 0.2409 0.2377 0.2815 0.2813 RANDOM 187.526
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] 3.51 3.51 -7.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_4_deg 16.844 r_dihedral_angle_3_deg 15.785 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.394 r_angle_other_deg 0.874 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_4_deg 16.844 r_dihedral_angle_3_deg 15.785 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.394 r_angle_other_deg 0.874 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5724 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction