2CN1

Crystal structure of Human Cytosolic 5'-Nucleotidase III (NT5C3)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.524% PEG1500, 20% GLYCEROL, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.5552

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.389α = 90
b = 100.951β = 90
c = 76.723γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2006-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.6776.799.90.0915.25.59828
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)
12.672.8199.80.364.25.7

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 2BDU2.6765.65934647099.90.1960.1920.267RANDOM42.12
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]
1.20.93-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.506
r_dihedral_angle_4_deg24.122
r_dihedral_angle_3_deg17.923
r_dihedral_angle_1_deg5.652
r_scangle_it3.345
r_scbond_it2.114
r_angle_refined_deg1.61
r_mcangle_it1.32
r_mcbond_it0.76
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.506
r_dihedral_angle_4_deg24.122
r_dihedral_angle_3_deg17.923
r_dihedral_angle_1_deg5.652
r_scangle_it3.345
r_scbond_it2.114
r_angle_refined_deg1.61
r_mcangle_it1.32
r_mcbond_it0.76
r_nbtor_refined0.313
r_symmetry_hbond_refined0.237
r_nbd_refined0.223
r_xyhbond_nbd_refined0.158
r_symmetry_vdw_refined0.148
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2188
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing