2J2C

Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BDEPDB ENTRY 2BDE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.8 M MG2SO4 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.1761.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.465α = 90
b = 128.034β = 90
c = 130.415γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2006-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.291.291000.0622.563921223.5
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)
12.22.321000.1511.56.2

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 2BDE2.2403723419671000.1540.1520.184RANDOM7.85
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]
-0.25-0.040.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.779
r_dihedral_angle_4_deg18.438
r_dihedral_angle_3_deg14.102
r_dihedral_angle_1_deg5.958
r_scangle_it3.171
r_scbond_it2.105
r_angle_refined_deg1.428
r_mcangle_it1.206
r_mcbond_it0.772
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.779
r_dihedral_angle_4_deg18.438
r_dihedral_angle_3_deg14.102
r_dihedral_angle_1_deg5.958
r_scangle_it3.171
r_scbond_it2.105
r_angle_refined_deg1.428
r_mcangle_it1.206
r_mcbond_it0.772
r_nbtor_refined0.303
r_nbd_refined0.193
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.139
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms3828
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing