7W3W

X-ray structure of apo-VmFbpA, a ferric ion-binding protein from Vibrio metschnikovii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WAE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293.150.25M ammonium tartrate dibasic, 25% PEG 3350, 100mM Tris-HCl (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.6653.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.792α = 90
b = 90.792β = 90
c = 149.836γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277.15PIXELDECTRIS EIGER X 16M2020-11-13MSINGLE WAVELENGTH
21x-ray277.15PIXELDECTRIS PILATUS 2M-F2020-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.899995SPring-8BL44XU
2SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.85845.43799.80.99915.177.8558147
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
21.861.970.999

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3WAE1.85845.43731428149999.7590.1860.1850.207927.803
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]
0.0180.0090.018-0.06
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2364
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
MOLREPphasing