2XCX

Crystal structure of the apoform of the D52N variant of cytosolic 5'- nucleotidase II


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 PH9.0, 10% PEG6000
Crystal Properties
Matthews coefficientSolvent content
3.1661

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.12α = 90
b = 126.51β = 90
c = 130.08γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDYNAMICALLY BENDABLE2008-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.32099.90.0717.375.534076-3
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)
12.32.41000.63.65.5

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 2JCM2.348.6832347172799.910.184760.182340.22901RANDOM44.2
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]
-1.210.740.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.498
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg17.109
r_dihedral_angle_1_deg6.631
r_scangle_it3.183
r_scbond_it2.192
r_angle_refined_deg1.548
r_mcangle_it1.326
r_mcbond_it0.796
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.498
r_dihedral_angle_4_deg18.137
r_dihedral_angle_3_deg17.109
r_dihedral_angle_1_deg6.631
r_scangle_it3.183
r_scbond_it2.192
r_angle_refined_deg1.548
r_mcangle_it1.326
r_mcbond_it0.796
r_nbtor_refined0.305
r_nbd_refined0.197
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.149
r_chiral_restr0.106
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 Atoms3805
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing