X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TPU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52938-10% PEG-8000, 1.25 M tetraethylammonium chloride, 2% dimethylsulfoxide, 5mM TDP
Crystal Properties
Matthews coefficientSolvent content
3.1861.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.953α = 90
b = 177.953β = 90
c = 88.6γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBRUKER PHOTON II CPAD2016-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEExcillum MetalJet D2+ 160 kV1.3418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.155099.30.0710.07111.47.139045
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)
12.152.2496.20.3622.85.4

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 REPLACEMENTTHROUGHOUT5TPU2.14125.8337071187999.090.209810.207090.26317RANDOM45.419
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]
-1.62-1.623.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.961
r_dihedral_angle_4_deg27.632
r_dihedral_angle_3_deg18.281
r_long_range_B_other11.127
r_long_range_B_refined11.102
r_scangle_other9.407
r_dihedral_angle_1_deg8.137
r_scbond_it7.055
r_scbond_other6.766
r_mcangle_it6.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.961
r_dihedral_angle_4_deg27.632
r_dihedral_angle_3_deg18.281
r_long_range_B_other11.127
r_long_range_B_refined11.102
r_scangle_other9.407
r_dihedral_angle_1_deg8.137
r_scbond_it7.055
r_scbond_other6.766
r_mcangle_it6.226
r_mcangle_other6.225
r_mcbond_it5.11
r_mcbond_other5.103
r_angle_refined_deg2.135
r_angle_other_deg0.954
r_chiral_restr0.134
r_bond_refined_d0.013
r_gen_planes_refined0.009
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 Atoms3408
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing