3PRP

Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PRMPDB ENTRY 3PRM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529822-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0540.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.316α = 90
b = 105.845β = 90
c = 113.032γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.978APS21-ID-F

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
11.69977.2696.50.05550853
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)
1.6991.7674.20.1862.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3PRM1.69977.2650853258196.540.1740.1720.212RANDOM25.511
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]
-1.2-0.431.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.731
r_dihedral_angle_4_deg17.176
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg5.881
r_scangle_it3.138
r_scbond_it1.985
r_angle_refined_deg1.351
r_mcangle_it1.136
r_mcbond_it0.625
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.731
r_dihedral_angle_4_deg17.176
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg5.881
r_scangle_it3.138
r_scbond_it1.985
r_angle_refined_deg1.351
r_mcangle_it1.136
r_mcbond_it0.625
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3788
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms8

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling