5FWI | pdb_00005fwi

structure of usp7 catalytic domain and three ubl-domains


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NB8PDB ENTRIES 1NB8, 2YLM
experimental modelPDB 2YLMPDB ENTRIES 1NB8, 2YLM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
115% PEG 3350 0.2M NA CITRATE
Crystal Properties
Matthews coefficientSolvent content
3.9268.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.183α = 90
b = 195.04β = 90
c = 219.78γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2014-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.448.7699.90.0613.44.5171982
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.671000.731.94.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1NB8, 2YLM3.4109.891634685199.820.224360.222210.220.266930.27RANDOM171.029
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]
7.841.47-9.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.283
r_dihedral_angle_4_deg17.983
r_dihedral_angle_3_deg13.978
r_dihedral_angle_1_deg6.328
r_mcangle_it2.372
r_mcbond_it1.313
r_mcbond_other1.312
r_angle_refined_deg1.278
r_scbond_it1.016
r_angle_other_deg0.925
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5352
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing