3CJ1

Structure of Rattus norvegicus NTPDase2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2277100mM NaHEPES, 2% PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3246.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.346α = 90
b = 69.029β = 90
c = 164.248γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID130.947ESRFID13

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
11.734.481000.07813.75.55297452974219.8
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)
1.71.791000.5132.85.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSIRASTHROUGHOUT1.733.7851660108699.910.175670.175070.20385RANDOM21.785
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]
0.490.25-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_dihedral_angle_4_deg13.08
r_dihedral_angle_3_deg12.631
r_dihedral_angle_1_deg5.456
r_scangle_it4.05
r_scbond_it2.671
r_mcangle_it1.565
r_angle_refined_deg1.43
r_mcbond_it1.096
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.895
r_dihedral_angle_4_deg13.08
r_dihedral_angle_3_deg12.631
r_dihedral_angle_1_deg5.456
r_scangle_it4.05
r_scbond_it2.671
r_mcangle_it1.565
r_angle_refined_deg1.43
r_mcbond_it1.096
r_nbtor_refined0.307
r_symmetry_vdw_refined0.208
r_nbd_refined0.201
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.107
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3294
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing