4KX3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FE3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION828320% PEG 3350, 0.10 M HEPES, 0.050 M Ammonium Acetate, VAPOR DIFFUSION, temperature 283K, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.3246.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.872α = 90
b = 46.872β = 90
c = 285.873γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2013-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.15099.90.1180.0866.913.819954199221220.425
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)
12.12.141000.58614.3998

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 REPLACEMENTTHROUGHOUT4FE32.146.921984899199.890.15610.15310.2165RANDOM28.3699
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]
0.320.32-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.081
r_dihedral_angle_4_deg17.827
r_dihedral_angle_3_deg14.336
r_dihedral_angle_1_deg5.938
r_angle_refined_deg1.759
r_angle_other_deg0.845
r_chiral_restr0.104
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.081
r_dihedral_angle_4_deg17.827
r_dihedral_angle_3_deg14.336
r_dihedral_angle_1_deg5.938
r_angle_refined_deg1.759
r_angle_other_deg0.845
r_chiral_restr0.104
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2326
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms61

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection