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
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.565α = 90
b = 118.748β = 90
c = 156.595γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.0594.698.80.140.180.0723.710.874311
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)
12.052.0989.70.340.430.210.8884.36.1

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 REPLACEMENTTHROUGHOUT3GFT2.0529.4770508372898.780.172210.171230.19061RANDOM30.906
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]
-0.360.9-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.257
r_dihedral_angle_4_deg15.342
r_dihedral_angle_3_deg13.911
r_long_range_B_refined8.746
r_long_range_B_other8.746
r_scangle_other6.587
r_dihedral_angle_1_deg6.078
r_scbond_it4.391
r_scbond_other4.384
r_mcangle_it4.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.257
r_dihedral_angle_4_deg15.342
r_dihedral_angle_3_deg13.911
r_long_range_B_refined8.746
r_long_range_B_other8.746
r_scangle_other6.587
r_dihedral_angle_1_deg6.078
r_scbond_it4.391
r_scbond_other4.384
r_mcangle_it4.377
r_mcangle_other4.377
r_mcbond_it3.161
r_mcbond_other3.161
r_angle_refined_deg1.574
r_angle_other_deg1.013
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_refined0.008
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 Atoms8134
Nucleic Acid Atoms
Solvent Atoms693
Heterogen Atoms237

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing