4GK6

X-ray crystal structure of a hypothetical deoxyuridine 5-triphosphate nucleotidohydrolase from Mycobacterium abscessus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MQ7pdb entry 1MQ7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52891 M Lithium chloride, 0.1 M sodium acetate, 30% PEG 6000, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.7455.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.26α = 90
b = 98.26β = 90
c = 98.26γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.9774ALS5.0.2

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
11.65501000.08414.591915419154-3-321.707
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)
11.651.691000.5453.27

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1MQ71.6540.15191541915498699.940.15980.15980.15860.1807RANDOM15.774
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_3_deg10.475
r_dihedral_angle_4_deg8.397
r_dihedral_angle_1_deg6.511
r_angle_refined_deg1.486
r_angle_other_deg0.744
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_3_deg10.475
r_dihedral_angle_4_deg8.397
r_dihedral_angle_1_deg6.511
r_angle_refined_deg1.486
r_angle_other_deg0.744
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms1

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction