X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WYG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22959-11% polyethylene glycol 8000, 0.6M Li2SO4, 5mM DTT, 1mM sodium salicylate, 0.4mM EDTA, 15% glycerol, 40mM HEPES (pH 6.20)
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.717α = 90
b = 138.084β = 90
c = 222.255γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
11.9438.891000.09520.27.2224074
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)
11.941.9999.460.249

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 REPLACEMENTTHROUGHOUT1WYG1.9438.892124821122299.820.174180.172370.20842RANDOM23.577
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
r_dihedral_angle_2_deg34.708
r_dihedral_angle_4_deg18.931
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg6.978
r_long_range_B_refined5.403
r_long_range_B_other5.403
r_scangle_other4.465
r_scbond_it2.992
r_scbond_other2.992
r_mcangle_other2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.708
r_dihedral_angle_4_deg18.931
r_dihedral_angle_3_deg14.301
r_dihedral_angle_1_deg6.978
r_long_range_B_refined5.403
r_long_range_B_other5.403
r_scangle_other4.465
r_scbond_it2.992
r_scbond_other2.992
r_mcangle_other2.84
r_mcangle_it2.838
r_mcbond_it2.039
r_mcbond_other2.022
r_angle_refined_deg1.626
r_angle_other_deg0.995
r_chiral_restr0.084
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 Atoms19890
Nucleic Acid Atoms
Solvent Atoms1290
Heterogen Atoms154

Software

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