☰ Navigation Tabs
Crystal Structure of USP2 in complex with mutated ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD5 pdb entry 2HD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 21% PEG 3350,0.2 M CaCl,
0.1 Bis-Tris pH 7.0,
glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.735 α = 90 b = 84.077 β = 90 c = 86.915 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN A200 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 84.08 97.4 0.0579 19.49 6.39 46959 45718
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 72.3 2.31 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 2HD5 1.7 84.08 46855 43314 2300 97.25 0.17844 0.1762 0.1757 0.22018 0.2216 RANDOM 21.477
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] -1.79 -0.16 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.329 r_scbond_it 2.054 r_angle_refined_deg 1.983 r_mcangle_it 1.544 r_mcbond_it 0.876 r_mcbond_other 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.232 r_dihedral_angle_4_deg 22.924 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.329 r_scbond_it 2.054 r_angle_refined_deg 1.983 r_mcangle_it 1.544 r_mcbond_it 0.876 r_mcbond_other 0.202 r_chiral_restr 0.151 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d r_angle_other_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3274 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 9
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing