4I1V

Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5289BuviA.00139.a.B1 PS01581 at 26.1 mg/mL with 2 mM ADP against Morpheus screen condition F1, 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each monosaccharide, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 237917f1, unique puck ID beh5-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.8768.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.86α = 90
b = 115.86β = 90
c = 91.64γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
12.65099.70.04626.185.22223022169-359.114
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)
12.62.6799.80.53.7

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 REPLACEMENTTHROUGHOUT4i1u2.644.0422169113099.730.21480.21280.2518RANDOM63.8381
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]
0.690.690.69-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.442
r_dihedral_angle_3_deg15.117
r_dihedral_angle_4_deg12.708
r_dihedral_angle_1_deg5.813
r_angle_refined_deg1.469
r_angle_other_deg0.954
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.442
r_dihedral_angle_3_deg15.117
r_dihedral_angle_4_deg12.708
r_dihedral_angle_1_deg5.813
r_angle_refined_deg1.469
r_angle_other_deg0.954
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2963
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms54

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction