3P0F

Structure of hUPP2 in an inactive conformation with bound 5-benzylacyclouridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EUFPBD ENTRY 3EUF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527720% polyvinylpyrrolidone K15, 0.1M cobalt chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5451.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.696α = 90
b = 59.696β = 90
c = 189.307γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.98SSRLBL7-1

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
11.545099.10.05513.26.651429
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)
11.541.693.10.482.74724

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 REPLACEMENTTHROUGHOUTPBD ENTRY 3EUF1.545051304260099.020.19170.19070.2124RANDOM21.4512
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]
0.290.29-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg12.112
r_dihedral_angle_1_deg5.434
r_scangle_it3.878
r_scbond_it2.479
r_mcangle_it1.602
r_angle_refined_deg1.392
r_mcbond_it1.025
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.889
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg12.112
r_dihedral_angle_1_deg5.434
r_scangle_it3.878
r_scbond_it2.479
r_mcangle_it1.602
r_angle_refined_deg1.392
r_mcbond_it1.025
r_nbtor_refined0.308
r_nbd_refined0.195
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.122
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2302
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms23

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction