X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EKI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295100 mM sodium HEPES pH 7.5, 28-32% (w/v) polyethylene glycol (PEG) 400, and 200-400 mM calcium chloride dehydrate.
Crystal Properties
Matthews coefficientSolvent content
2.5251.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.885α = 90
b = 109.034β = 90
c = 123.186γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELDECTRIS PILATUS3 S 6M2018-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C1.0PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.6123.1997.90.0830.9559.83.447255
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.690.3180.758

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 REPLACEMENTTHROUGHOUT6EKI2.6123.1947255247897.540.191830.189930.22719RANDOM43.941
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]
-0.880.623.63-2.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_3_deg16.888
r_dihedral_angle_4_deg13.86
r_long_range_B_other8.486
r_long_range_B_refined8.484
r_scangle_other6.625
r_dihedral_angle_1_deg6.569
r_mcangle_it4.704
r_mcangle_other4.704
r_scbond_it4.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_3_deg16.888
r_dihedral_angle_4_deg13.86
r_long_range_B_other8.486
r_long_range_B_refined8.484
r_scangle_other6.625
r_dihedral_angle_1_deg6.569
r_mcangle_it4.704
r_mcangle_other4.704
r_scbond_it4.134
r_scbond_other4.133
r_mcbond_it3.026
r_mcbond_other3.026
r_angle_refined_deg1.814
r_angle_other_deg1.103
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms10818
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms110

Software

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