2XJD

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JCMPDB ENTRY 2JCM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M BICINE PH 9, 10% PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.1661

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.299α = 90
b = 128.432β = 90
c = 131.201γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
1265.651000.1410.6552910
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)
122.111000.545

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 2JCM264.2850236267399.990.177570.175920.20821RANDOM20.596
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]
0.66-0.08-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.498
r_dihedral_angle_4_deg18.916
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.016
r_scangle_it3.18
r_scbond_it2.201
r_mcangle_it1.454
r_angle_refined_deg1.335
r_mcbond_it0.965
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.498
r_dihedral_angle_4_deg18.916
r_dihedral_angle_3_deg13.557
r_dihedral_angle_1_deg6.016
r_scangle_it3.18
r_scbond_it2.201
r_mcangle_it1.454
r_angle_refined_deg1.335
r_mcbond_it0.965
r_nbtor_refined0.301
r_nbd_refined0.187
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.134
r_chiral_restr0.096
r_bond_refined_d0.015
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 Atoms3768
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling