4FE3

Structure of murine cytosolic 5'-nucleotidase III complexed with uridinine monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BDUPDB ENTRY 2BDU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828320% PEG 3350, 100 mM TRIS, 50 mM ammonium acetate , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.3347.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.878α = 90
b = 46.878β = 90
c = 287.101γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2010-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.98APS21-ID-D

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.745098.30.080.06332.1717.9339806072461121.8
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)RedundancyNumber Unique Reflections (All)
11.741.7797.10.5550.5314.897.11581

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BDU1.74503398033814171098.130.17170.17170.16930.2185RANDOM25.2494
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]
0.030.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.6
r_dihedral_angle_3_deg14.524
r_dihedral_angle_4_deg14.025
r_dihedral_angle_1_deg5.826
r_angle_refined_deg1.356
r_chiral_restr0.119
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2326
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms31

Software

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