3AI7 | pdb_00003ai7

Crystal Structure of Bifidobacterium Longum Phosphoketolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherthe roughly refined crystal structure of the selenomethionine substituted protein

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop6.6299PEG3350, MES, Sodium thiocyanate, pH 6.6, hanging drop, temperature 299K
Crystal Properties
Matthews coefficientSolvent content
2.7455.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.26α = 90
b = 184.41β = 97.31
c = 157.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A

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
12.2156.1698.90.085401973-328.555
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)
12.22.393.40.294.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTthe roughly refined crystal structure of the selenomethionine substituted protein2.247.873817432023098.880.149810.146870.150.205520.21RANDOM24.12
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]
-0.17-2.4-1.481.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.188
r_dihedral_angle_4_deg17.854
r_dihedral_angle_3_deg15.56
r_dihedral_angle_1_deg6.926
r_scangle_it4.865
r_scbond_it3.208
r_angle_refined_deg1.933
r_mcangle_it1.825
r_mcbond_it1.055
r_chiral_restr0.136
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms51680
Nucleic Acid Atoms
Solvent Atoms5056
Heterogen Atoms216

Software

Software
Software NamePurpose
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction