2PKM

Crystal structure of M tuberculosis Adenosine Kinase complexed with 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
2.3246.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.9α = 90
b = 71.9β = 90
c = 110.8γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVOsmic mirrors2006-03-05MSINGLE 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
11.962.6697.840.042485524855
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94997.33

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 ADK1.962.2624855129997.840.219350.217230.25956RANDOM41.134
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.423
r_dihedral_angle_4_deg17.533
r_dihedral_angle_3_deg13.83
r_dihedral_angle_1_deg6.091
r_scangle_it5.746
r_scbond_it4.331
r_mcangle_it3.308
r_mcbond_it2.458
r_angle_refined_deg1.336
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.423
r_dihedral_angle_4_deg17.533
r_dihedral_angle_3_deg13.83
r_dihedral_angle_1_deg6.091
r_scangle_it5.746
r_scbond_it4.331
r_mcangle_it3.308
r_mcbond_it2.458
r_angle_refined_deg1.336
r_nbtor_refined0.3
r_symmetry_hbond_refined0.226
r_symmetry_vdw_refined0.204
r_nbd_refined0.2
r_xyhbond_nbd_refined0.133
r_chiral_restr0.101
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2444
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing