2JAR

Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN) in complex with deoxyuridine 5'- monophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52790.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS PH 5.5, 23-25% PEG3350 AT 6 DEGREES CELSIUS
Crystal Properties
Matthews coefficientSolvent content
3.261.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.309α = 90
b = 75.309β = 90
c = 85.174γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-02-25MSINGLE 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
11.9565.231000.11910.720062
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)
11.952.061000.345.810.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.94401930710341000.1580.1560.201RANDOM24.74
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]
-0.05-0.03-0.050.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg17.138
r_dihedral_angle_3_deg13.849
r_dihedral_angle_1_deg6.041
r_scangle_it3.685
r_scbond_it3.233
r_mcangle_it1.727
r_angle_refined_deg1.423
r_mcbond_it1.201
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg17.138
r_dihedral_angle_3_deg13.849
r_dihedral_angle_1_deg6.041
r_scangle_it3.685
r_scbond_it3.233
r_mcangle_it1.727
r_angle_refined_deg1.423
r_mcbond_it1.201
r_nbtor_refined0.302
r_nbd_refined0.191
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.139
r_chiral_restr0.1
r_bond_refined_d0.014
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_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 Atoms1595
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing