3P4I

Crystal structure of acetate kinase from Mycobacterium avium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TUYpdb entry 1tuy

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289protein at 23.4 mg/mL, 10 % PEG 8000, 0.1 M Tris pH 7.0, 0.1 M MgCl2 with 25% ethylene glycol as cryo-protectant, crsytal tracking ID 216702h7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.7655.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.64α = 90
b = 101.71β = 90
c = 105.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97946ALS5.0.3

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
12.355099.70.09812.155.43917239051-342.778
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)
12.352.411000.5313.4

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 REPLACEMENTTHROUGHOUTpdb entry 1tuy2.355038908194699.350.18470.18230.2298RANDOM37.2275
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]
-1.492.82-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.778
r_dihedral_angle_4_deg18.663
r_dihedral_angle_3_deg15.904
r_dihedral_angle_1_deg5.754
r_scangle_it3.146
r_scbond_it1.854
r_angle_refined_deg1.472
r_mcangle_it1.161
r_mcbond_it0.614
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.778
r_dihedral_angle_4_deg18.663
r_dihedral_angle_3_deg15.904
r_dihedral_angle_1_deg5.754
r_scangle_it3.146
r_scbond_it1.854
r_angle_refined_deg1.472
r_mcangle_it1.161
r_mcbond_it0.614
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5633
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms4

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction