X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TRX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Crystals were obtained with a protein concentration of 20-25 mg/ml. The composition of the reservoir solution was 17% (w/v) PEG10000, 0.1 M ammonium acetate and 0.1 M BIS-TRIS buffer, pH 5.5.
Crystal Properties
Matthews coefficientSolvent content
4.4172.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.34α = 90
b = 95.34β = 90
c = 39.646γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442014-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.9982.5793.60.07914.82.77669
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.993.13

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2TRX2.9982.57669596393.60.205830.197610.25945RANDOM53.326
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.548
r_dihedral_angle_4_deg23.803
r_dihedral_angle_3_deg18.795
r_long_range_B_refined8.232
r_long_range_B_other8.232
r_dihedral_angle_1_deg6.712
r_scangle_other5.611
r_mcangle_it5.322
r_mcangle_other5.32
r_scbond_it3.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.548
r_dihedral_angle_4_deg23.803
r_dihedral_angle_3_deg18.795
r_long_range_B_refined8.232
r_long_range_B_other8.232
r_dihedral_angle_1_deg6.712
r_scangle_other5.611
r_mcangle_it5.322
r_mcangle_other5.32
r_scbond_it3.325
r_scbond_other3.324
r_mcbond_other3.234
r_mcbond_it3.232
r_angle_refined_deg1.496
r_angle_other_deg0.798
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1656
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing