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WDR48 (2-580):USP46~ubiquitin ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CVL PDB entries 5CVL, 1NBF experimental model PDB 1NBF PDB entries 5CVL, 1NBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 292 0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8
Crystal Properties Matthews coefficient Solvent content 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.437 α = 90 b = 154.189 β = 90 c = 182.854 γ = 90
Symmetry Space Group I 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 CCD ADSC QUANTUM 315 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 3.35 47.36 21052 87.8
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 3.35 3.47 99.9 0.719 7.7 2064
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 5CVL, 1NBF 3.36 47.36 21052 1060 99.19 0.1772 0.1749 0.1824 0.2219 0.232 RANDOM 103.39
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] 17.7952 -0.2457 -17.5495
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.89 t_omega_torsion 2.59 t_angle_deg 1.17 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.89 t_omega_torsion 2.59 t_angle_deg 1.17 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7288 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 1
Software Software Software Name Purpose BUSTER refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing