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Structure of USP21 in complex with linear diubiquitin-aldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD5 PDB ENTRIES 2HD5 AND 1UBQ experimental model PDB 1UBQ PDB ENTRIES 2HD5 AND 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 15% PEG8000, 0.2 M NH4SO4, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.87 α = 90 b = 102.2 β = 99.82 c = 86.8 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 CCD MARRESEARCH 2009-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.7 49.8 91.1 0.12 8.8 2.9 24840 2 42.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 86.2 0.47 2.4 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2HD5 AND 1UBQ 2.7 45 23530 1267 90.3 0.21898 0.2158 0.27859 0.2489 RANDOM 20.315
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] -0.76 0.15 1.23 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 17.89 r_dihedral_angle_3_deg 17.497 r_dihedral_angle_1_deg 5.132 r_angle_refined_deg 1.035 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 17.89 r_dihedral_angle_3_deg 17.497 r_dihedral_angle_1_deg 5.132 r_angle_refined_deg 1.035 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7093 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing