2R9Q

Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62950.2M CaCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
2.2946.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.693α = 90
b = 129.042β = 108.75
c = 85.559γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-08-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97940, 0.97960APS19-ID

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
12.246.7893.90.09917.14.17358869099257
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)
12.22.2653.360.6470.81.75433

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.246.78690996909969093.90.18980.18980.189040.26949RANDOM56.968
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]
0.19-0.38-0.12-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.399
r_dihedral_angle_4_deg17.045
r_dihedral_angle_3_deg16.596
r_dihedral_angle_1_deg7.218
r_scangle_it3.741
r_scbond_it2.579
r_mcangle_it1.851
r_angle_refined_deg1.521
r_mcbond_it1.153
r_angle_other_deg1.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.399
r_dihedral_angle_4_deg17.045
r_dihedral_angle_3_deg16.596
r_dihedral_angle_1_deg7.218
r_scangle_it3.741
r_scbond_it2.579
r_mcangle_it1.851
r_angle_refined_deg1.521
r_mcbond_it1.153
r_angle_other_deg1.057
r_mcbond_other0.355
r_nbd_other0.207
r_nbd_refined0.189
r_symmetry_vdw_other0.18
r_xyhbond_nbd_refined0.18
r_xyhbond_nbd_other0.174
r_nbtor_refined0.172
r_symmetry_vdw_refined0.17
r_symmetry_hbond_refined0.11
r_chiral_restr0.088
r_nbtor_other0.087
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10146
Nucleic Acid Atoms
Solvent Atoms622
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing