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Structure of a USP8-NRDP1 complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 12% PEG5000 MME, 0.1 M bis-Tris, 1 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.111 α = 90 b = 67.094 β = 91.12 c = 99.275 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 ADSC QUANTUM 210 2006-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9800 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 30 93.4 0.069 21.98 4 41906 41906 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 97.8 0.46 3.15 4 4352
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 2.3 30 39572 2093 93.17 0.20767 0.2061 0.2009 0.23704 0.2351 RANDOM 29.84
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] 2.7 -1.11 -1.62 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 5.593 r_scangle_it 2.234 r_scbond_it 1.439 r_mcangle_it 1.201 r_angle_refined_deg 1.191 r_mcbond_it 0.746 r_nbtor_refined 0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.888 r_dihedral_angle_4_deg 16.159 r_dihedral_angle_3_deg 15.209 r_dihedral_angle_1_deg 5.593 r_scangle_it 2.234 r_scbond_it 1.439 r_mcangle_it 1.201 r_angle_refined_deg 1.191 r_mcbond_it 0.746 r_nbtor_refined 0.288 r_nbd_refined 0.168 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6170 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling SOLVE phasing