4EBU | pdb_00004ebu

Crystal structure of a sugar kinase (Target EFI-502312) from Oceanicola granulosus, with bound AMP/ADP crystal form I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E69PDB ENTRY 4E69

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4298protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.1 M sodium acetate, pH 4.6, 1.5 M ammonium chloride), cryoprotection (reservoir + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0860.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.308α = 90
b = 94.308β = 90
c = 82.959γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEmirrors2012-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
1282.95999.50.1170.1178.55.42908129081
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)
122.111000.6650.6651.15.44209

Refinement

Statistics
Diffraction IDStructure Solution 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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4E69236.6382901829018147399.360.1790.1790.17720.180.21520.22RANDOM39.7392
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]
8.25598.2559-16.5117
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.172
f_angle_d1.094
f_chiral_restr0.072
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2255
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms51

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
PHENIXphasing