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Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W6V pdb entry 1W6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 1 volume of 9 mg/ml protein solution was mixed with 1 volume of a solution of 20% (w/v) PEG 4000, 10% (v/v) isopropanool, 0.1 M sodium HEPES, and 0.001 M dithiothreitol and equilibrated against 1 M NaCl (well solution). The crystal was cryoprotected in well solution mixed 1:1 with a solution containing 60% (v/v) ethylene glycol and 200 mg/ml 3-(1-pyridino)-propene sulfonate (NDSB-201) and frozen by immersion in liquid nitrogen, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.06 α = 90 b = 34.06 β = 133.52 c = 125.19 γ = 90
Symmetry Space Group C 1 2 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 Si(111) double-crystal monochromator 2006-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97942 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.37 45.4 99.1 0.096 0.104 11.9 6.9 22820 22745 3 39.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.37 2.5 98.4 0.349 0.38 4.1 6.5 3246
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MRSAD pdb entry 1W6V 2.37 41.227 1.37 22421 1110 97.39 0.1844 0.1819 0.1761 0.2334 0.2245 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.658 f_angle_d 1.062 f_chiral_restr 0.07 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3523 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 13
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX model building SHARP phasing PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing