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Structure of the D1D2 domain of USP4, the conserved catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GFO PDB ENTRY 2GFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN WAS CRYSTALLIZED FROM 100MM BIS-TRIS PROPANE (PH8.5), 25MM NA2SO4, 18% PEG3350, THEN SOAKED IN 25% ETHYLENEGLYCOL
Crystal Properties Matthews coefficient Solvent content 2.94 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.5 α = 90 b = 151.03 β = 90 c = 178.67 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 ADSC QUANTUM 4 MIRRORS 2009-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.4 44.6 94.9 0.09 11 3.4 111095 1.1 53.38
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 2.4 44.6 74 0.66 1.4 2.4
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 ENTRY 2GFO 2.4 44.59 111095 5583 0.1797 0.178 0.2104 0.1985 RANDOM 52.31
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] 4.2468 -2.383 -1.8638
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.05 t_other_torsion 2.88 t_angle_deg 1.02 t_bond_d 0.01 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_omega_torsion 3.05 t_other_torsion 2.88 t_angle_deg 1.02 t_bond_d 0.01 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 15933 Nucleic Acid Atoms Solvent Atoms 1249 Heterogen Atoms 16
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling PHASER phasing