X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.5-3 M Na malonate, 0.1 M Tris.acetate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.18α = 90
b = 91.51β = 131.34
c = 99.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.97625DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.6671.05980.0830.0890.997126.1117045
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.799.31.0291.2010.5430.93.7

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 REPLACEMENTTHROUGHOUT5A8B1.6671.05111245574797.90.203890.203030.221RANDOM36.452
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]
-0.34-0.031.49-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.814
r_dihedral_angle_3_deg15.257
r_dihedral_angle_4_deg13.434
r_long_range_B_refined6.902
r_long_range_B_other6.902
r_dihedral_angle_1_deg6.471
r_scangle_other3.327
r_mcangle_it2.293
r_mcangle_other2.293
r_scbond_it2.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.814
r_dihedral_angle_3_deg15.257
r_dihedral_angle_4_deg13.434
r_long_range_B_refined6.902
r_long_range_B_other6.902
r_dihedral_angle_1_deg6.471
r_scangle_other3.327
r_mcangle_it2.293
r_mcangle_other2.293
r_scbond_it2.101
r_scbond_other2.101
r_angle_refined_deg1.66
r_mcbond_it1.431
r_mcbond_other1.431
r_angle_other_deg1.421
r_chiral_restr0.085
r_bond_refined_d0.011
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 Atoms4180
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing