X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.150.1 M Bicine-Tris, 8% PEG1000, 8% PEG3350, 8% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.2344.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.965α = 90
b = 108.291β = 90
c = 115.621γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.977021ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5482.9799.90.1170.9848.96.5153937
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.5799.50.9070.5351.76.4

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 REPLACEMENTTHROUGHOUT5ELB1.5479.16146128767699.820.194110.192550.22355RANDOM18.474
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]
-0.1-1.171.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.01
r_dihedral_angle_4_deg30.36
r_dihedral_angle_1_deg15.589
r_dihedral_angle_3_deg14.225
r_long_range_B_refined3.638
r_long_range_B_other3.638
r_angle_refined_deg1.686
r_scangle_other1.662
r_mcangle_it1.205
r_mcangle_other1.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.01
r_dihedral_angle_4_deg30.36
r_dihedral_angle_1_deg15.589
r_dihedral_angle_3_deg14.225
r_long_range_B_refined3.638
r_long_range_B_other3.638
r_angle_refined_deg1.686
r_scangle_other1.662
r_mcangle_it1.205
r_mcangle_other1.205
r_scbond_it1.074
r_scbond_other1.073
r_angle_other_deg1.008
r_mcbond_it0.755
r_mcbond_other0.755
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms8140
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms419

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
Cootmodel building
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing