3KM3

Crystal structure of eoxycytidine triphosphate deaminase from anaplasma phagocytophilum at 2.1A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.1290MD PACT SCREEN CONDITION D9: 100MM TRIS PH 8.1, 200MM LICL, 20% PEG 3350; ANPHA.00973.A AT XXMG/ ML, CRYSTAL SOAKED IN 100MM HEPES PH 7.0, 200MM NACL, 20% PEG 3350, 1M KI, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.1241.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.66α = 90
b = 84.66β = 90
c = 140.74γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442009-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.12098.90.07523.991121725-333.4
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)
12.12.1596.60.4475.19.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.1202187620752112499.60.1840.1820.222RANDOM12.62
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]
0.490.240.49-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.586
r_dihedral_angle_4_deg22.253
r_dihedral_angle_3_deg14.899
r_dihedral_angle_1_deg6.299
r_scangle_it3.426
r_scbond_it2.353
r_angle_refined_deg1.525
r_mcangle_it1.39
r_angle_other_deg0.878
r_mcbond_it0.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.586
r_dihedral_angle_4_deg22.253
r_dihedral_angle_3_deg14.899
r_dihedral_angle_1_deg6.299
r_scangle_it3.426
r_scbond_it2.353
r_angle_refined_deg1.525
r_mcangle_it1.39
r_angle_other_deg0.878
r_mcbond_it0.771
r_mcbond_other0.226
r_chiral_restr0.093
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2444
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms16

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling