2I5B

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UB0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529028% peg 4000, 0.17M sodium acetate trihydrate, 0.1M Tris HCL (pH 8.5), 10mM MgCl, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2745.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.499α = 90
b = 102.499β = 90
c = 251.36γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.894.91699.40.1310.1315.73.7336043360450.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9599.90.4750.4751.73.84844

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UB02.812.873330533305168899.430.2250.2250.2220.274RANDOM31.436
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.85
r_dihedral_angle_4_deg25.038
r_dihedral_angle_3_deg18.133
r_dihedral_angle_1_deg6.295
r_scangle_it1.936
r_angle_refined_deg1.455
r_scbond_it1.145
r_mcangle_it0.991
r_mcbond_it0.576
r_symmetry_hbond_refined0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.85
r_dihedral_angle_4_deg25.038
r_dihedral_angle_3_deg18.133
r_dihedral_angle_1_deg6.295
r_scangle_it1.936
r_angle_refined_deg1.455
r_scbond_it1.145
r_mcangle_it0.991
r_mcbond_it0.576
r_symmetry_hbond_refined0.43
r_symmetry_vdw_refined0.358
r_nbtor_refined0.311
r_nbd_refined0.219
r_xyhbond_nbd_refined0.13
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9932
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms135

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing