X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OAM2OAM, 2AQJ, 2WEU, 5HY5
experimental modelPDB 2AQJ2OAM, 2AQJ, 2WEU, 5HY5
experimental modelPDB 2WEU2OAM, 2AQJ, 2WEU, 5HY5
experimental modelPDB 5HY52OAM, 2AQJ, 2WEU, 5HY5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293reservoir: 0.1 M Tris pH 8.5, 1.5 M K2HPO4/KH2PO4 protein concentration: ~ 15mg/mL drop ratio: 2:1 (P:R) protein buffer: 10 mM Tris pH 7.4, 50 mM NaCl and 1 mM TCEP
Crystal Properties
Matthews coefficientSolvent content
3.2562.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.47α = 90
b = 139.47β = 90
c = 142.51γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9PETRA III, EMBL c/o DESYP13 (MX1)

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
12.249.891000.140.99811.58.57965452.9
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)
12.22.261001.8410.63428.4

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 REPLACEMENTTHROUGHOUT2OAM, 2AQJ, 2WEU, 5HY52.249.8975624399099.970.171680.169660.2111RANDOM48.75
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]
0.530.260.53-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.179
r_dihedral_angle_4_deg19.72
r_dihedral_angle_3_deg15.117
r_long_range_B_other9.124
r_long_range_B_refined9.121
r_scangle_other7.403
r_dihedral_angle_1_deg6.706
r_mcangle_it5.714
r_mcangle_other5.714
r_scbond_it5.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.179
r_dihedral_angle_4_deg19.72
r_dihedral_angle_3_deg15.117
r_long_range_B_other9.124
r_long_range_B_refined9.121
r_scangle_other7.403
r_dihedral_angle_1_deg6.706
r_mcangle_it5.714
r_mcangle_other5.714
r_scbond_it5.184
r_scbond_other5.182
r_mcbond_other4.118
r_mcbond_it4.117
r_angle_refined_deg1.457
r_angle_other_deg0.931
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.007
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 Atoms8376
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing