3CJA

Structure of Rattus norvegicus NTPDase2 in complex with calcium and AMPPNP


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
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.9α = 90
b = 68.87β = 90
c = 163.72γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
12.126.6796.30.11812.64.726670225.1
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)
2.12.210.42634.1

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 DIFFRACTIONSIRASTHROUGHOUT2.126.3425565108295.580.166590.164660.20994RANDOM22.66
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]
0.340.73-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_4_deg14.48
r_dihedral_angle_3_deg13.413
r_dihedral_angle_1_deg6.06
r_scangle_it3.184
r_scbond_it2.04
r_angle_refined_deg1.391
r_mcangle_it1.243
r_mcbond_it0.807
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_4_deg14.48
r_dihedral_angle_3_deg13.413
r_dihedral_angle_1_deg6.06
r_scangle_it3.184
r_scbond_it2.04
r_angle_refined_deg1.391
r_mcangle_it1.243
r_mcbond_it0.807
r_nbtor_refined0.301
r_nbd_refined0.196
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.127
r_metal_ion_refined0.1
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_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 Atoms3271
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing