X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IHM2IHM (molecule B) was used as the starting molecule for molecular replacement for a lower resolution structure, which was then used as the starting model for the current higher resolution structure.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8295Crystals were grown by mixing 1 uL of concentrated protein (10.7mg/mL) with 1 uL of mother liquor (50 mM imidazole pH 8, 0.8M sodium citrate) at room temperature, using the hanging drop vapor diffusion technique. The crystals reached usable size within 24 hours, and were then directly transferred to a cryoprotectant solution containing 50mM imidazole pH 8, 75mM NaCl, 1M sodium citrate, 10% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4349.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.192α = 90
b = 124.192β = 90
c = 50.407γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 92VariMaxHF mirrors2012-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8495099.30.05616.493412134121-322.27
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)
11.851.9296.40.4144.83245

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2IHM (molecule B) was used as the starting molecule for molecular replacement for a lower resolution structure, which was then used as the starting model for the current higher resolution structure.1.84925.8561.343412134070170899.340.18090.2283random19.6347
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.08
f_angle_d1.28
f_chiral_restr0.094
f_bond_d0.011
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2616
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms11

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection