2JC9

Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J2CPDB ENTRY 2J2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.51.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.273α = 90
b = 127.983β = 90
c = 130.601γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-10-08MSINGLE 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
11.574.951000.0817.66.4122218
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)
11.51.581000.442.33.7

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 2J2C1.574.3311571561171000.1620.160.186RANDOM16.18
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]
0.18-0.17-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.804
r_dihedral_angle_4_deg16.754
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg5.739
r_scangle_it3.686
r_scbond_it2.822
r_mcangle_it1.871
r_mcbond_it1.576
r_angle_refined_deg1.405
r_angle_other_deg0.887
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.804
r_dihedral_angle_4_deg16.754
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg5.739
r_scangle_it3.686
r_scbond_it2.822
r_mcangle_it1.871
r_mcbond_it1.576
r_angle_refined_deg1.405
r_angle_other_deg0.887
r_symmetry_vdw_refined0.441
r_symmetry_vdw_other0.359
r_nbd_refined0.217
r_nbd_other0.19
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.149
r_chiral_restr0.089
r_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3808
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing