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structure of usp7 catalytic domain and three ubl-domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB8 PDB ENTRIES 1NB8, 2YLM experimental model PDB 2YLM PDB ENTRIES 1NB8, 2YLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG 3350 0.2M NA CITRATE
Crystal Properties Matthews coefficient Solvent content 3.92 68.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.183 α = 90 b = 195.04 β = 90 c = 219.78 γ = 90
Symmetry Space Group F 2 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 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 3.4 48.76 99.9 0.06 13.4 4.5 17198 2
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 3.4 3.67 100 0.73 1.9 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1NB8, 2YLM 3.4 109.89 16346 851 99.82 0.22436 0.22221 0.2248 0.26693 0.2679 RANDOM 171.029
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] 7.84 1.47 -9.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.283 r_dihedral_angle_4_deg 17.983 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.328 r_mcangle_it 2.372 r_mcbond_it 1.313 r_mcbond_other 1.312 r_angle_refined_deg 1.278 r_scbond_it 1.016 r_angle_other_deg 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.283 r_dihedral_angle_4_deg 17.983 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 6.328 r_mcangle_it 2.372 r_mcbond_it 1.313 r_mcbond_other 1.312 r_angle_refined_deg 1.278 r_scbond_it 1.016 r_angle_other_deg 0.925 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_mcangle_other 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 5352 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing