X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GFT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2778-15% w/v polyethylene glycol 3350 and 0.2 M Lithium citrate
Crystal Properties
Matthews coefficientSolvent content
2.4950.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.187α = 90
b = 118.032β = 90
c = 156.371γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.21561000.0970.1080.0470.99815.69.660229
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2699.80.830.9390.430.9083.38.8

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 REPLACEMENTTHROUGHOUT3GFT2.294.2157101301699.860.203020.201610.23026RANDOM40.235
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]
-1.23.24-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_3_deg15.173
r_dihedral_angle_4_deg14.068
r_long_range_B_refined9.94
r_long_range_B_other9.939
r_scangle_other8.279
r_dihedral_angle_1_deg5.993
r_mcangle_it5.459
r_mcangle_other5.459
r_scbond_other5.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_3_deg15.173
r_dihedral_angle_4_deg14.068
r_long_range_B_refined9.94
r_long_range_B_other9.939
r_scangle_other8.279
r_dihedral_angle_1_deg5.993
r_mcangle_it5.459
r_mcangle_other5.459
r_scbond_other5.269
r_scbond_it5.268
r_mcbond_it3.707
r_mcbond_other3.706
r_angle_refined_deg1.45
r_angle_other_deg0.481
r_chiral_restr0.062
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 Atoms7779
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing