2PKK

Crystal structure of M tuberculosis Adenosine Kinase complexed with 2-fluro adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PKFapo MTB ADK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5290Crystals were obtained in conditions containing 0.1 M HEPES-Na, pH 7.5 and 1.4 M trisodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.916α = 90
b = 71.916β = 90
c = 110.521γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV2006-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.5412

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
11.9362.2699.60.082398223982
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)
11.931.9899.10.19

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTapo MTB ADK1.9362.2623982128999.670.191650.189080.23958RANDOM34.247
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]
0.040.020.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.845
r_dihedral_angle_4_deg20.918
r_dihedral_angle_3_deg14.185
r_scangle_it7.58
r_dihedral_angle_1_deg6.281
r_scbond_it5.644
r_mcangle_it4.059
r_mcbond_it3.124
r_angle_refined_deg1.486
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.845
r_dihedral_angle_4_deg20.918
r_dihedral_angle_3_deg14.185
r_scangle_it7.58
r_dihedral_angle_1_deg6.281
r_scbond_it5.644
r_mcangle_it4.059
r_mcbond_it3.124
r_angle_refined_deg1.486
r_nbtor_refined0.305
r_symmetry_hbond_refined0.225
r_nbd_refined0.214
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.146
r_chiral_restr0.112
r_bond_refined_d0.012
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2455
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing