2JAS | pdb_00002jas

Structure of deoxyadenosine kinase from M.mycoides with bound dATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5ZPDB ENTRY 1P5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1724% PEG 3350 0.2 M KSCN, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.845α = 90
b = 100.85β = 124.58
c = 109.486γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2004-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.747.11000.0815.63.6469412
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)
12.72.851000.42.93.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1P5Z2.74744555237299.70.2350.2330.230.2740.27RANDOM40.39
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]
-1.26-0.532.2-1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.548
r_dihedral_angle_4_deg21.863
r_dihedral_angle_3_deg17.323
r_dihedral_angle_1_deg5.14
r_angle_refined_deg1.143
r_scangle_it1.058
r_scbond_it0.654
r_mcangle_it0.536
r_nbtor_refined0.304
r_mcbond_it0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.548
r_dihedral_angle_4_deg21.863
r_dihedral_angle_3_deg17.323
r_dihedral_angle_1_deg5.14
r_angle_refined_deg1.143
r_scangle_it1.058
r_scbond_it0.654
r_mcangle_it0.536
r_nbtor_refined0.304
r_mcbond_it0.301
r_nbd_refined0.199
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.104
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms9715
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing