4F6T

The crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OGXPDB entry 2OGX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6277NH4H2PO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2VAPOR DIFFUSION, SITTING DROP5.6283NH4H2PO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.74α = 90
b = 115.74β = 90
c = 233.62γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-03-03MSINGLE WAVELENGTH
22x-ray100CCDADSC QUANTUM 315r2010-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.008SLSX10SA
2SYNCHROTRONESRF BEAMLINE ID291.71ESRFID29

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
1,21.646900.08513.454.4121767109553-322.705
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)
1,21.61.759.40.5483.61

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUTPDB entry 2OGX1.646-3121767109551546789.990.14210.14210.13940.1733RANDOM22.3128
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]
-0.09-0.05-0.090.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.965
r_dihedral_angle_4_deg16.84
r_dihedral_angle_3_deg13.894
r_scangle_it8.005
r_dihedral_angle_1_deg6.185
r_angle_refined_deg5.8
r_scbond_it5.727
r_mcangle_it3.927
r_rigid_bond_restr3.047
r_mcbond_it2.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.965
r_dihedral_angle_4_deg16.84
r_dihedral_angle_3_deg13.894
r_scangle_it8.005
r_dihedral_angle_1_deg6.185
r_angle_refined_deg5.8
r_scbond_it5.727
r_mcangle_it3.927
r_rigid_bond_restr3.047
r_mcbond_it2.668
r_chiral_restr0.322
r_bond_refined_d0.031
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3800
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms172

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
EDNAdata collection
XDSdata reduction
REFMACphasing