2PKN

Crystal structure of M tuberculosis Adenosine Kinase complexed with AMP-PCP (non-hydrolyzable ATP analog)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529020% PEG 8000, 100 mM sodium cacodylate pH 6.5, and 200 mM magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4750.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.05α = 90
b = 75.184β = 109.8
c = 52.38γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV2006-11-15MSINGLE 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
11.957.5499.870.052599125991

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 ADK1.957.5425991137999.870.20950.206860.25781RANDOM34.41
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]
-1.68-1.111.04-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.088
r_dihedral_angle_4_deg20.99
r_dihedral_angle_3_deg13.871
r_dihedral_angle_1_deg6.218
r_scangle_it6.024
r_scbond_it4.389
r_mcangle_it3.367
r_mcbond_it2.486
r_angle_refined_deg1.275
r_symmetry_hbond_refined0.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.088
r_dihedral_angle_4_deg20.99
r_dihedral_angle_3_deg13.871
r_dihedral_angle_1_deg6.218
r_scangle_it6.024
r_scbond_it4.389
r_mcangle_it3.367
r_mcbond_it2.486
r_angle_refined_deg1.275
r_symmetry_hbond_refined0.377
r_nbtor_refined0.293
r_symmetry_vdw_refined0.25
r_nbd_refined0.185
r_xyhbond_nbd_refined0.156
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2400
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement