X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I15 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% PEG 3350, 0.4 M sodium formate, 0.3 guanidine, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.467α = 90
b = 114.814β = 108.23
c = 68.314γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2016-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97622DiamondI03

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
11.7757.498.60.0550.0660.0350.99912.13.480974
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)
11.771.899.30.6150.7340.3970.7412.23.3

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 REPLACEMENTTHROUGHOUT4I151.7757.476961401298.560.161240.159480.19521RANDOM32.441
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]
3.16-0.44-0.9-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.661
r_dihedral_angle_4_deg14.533
r_dihedral_angle_3_deg14.254
r_long_range_B_refined7.409
r_long_range_B_other7.4
r_scangle_other6.055
r_dihedral_angle_1_deg5.551
r_scbond_it4.098
r_scbond_other4.098
r_mcangle_it3.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.661
r_dihedral_angle_4_deg14.533
r_dihedral_angle_3_deg14.254
r_long_range_B_refined7.409
r_long_range_B_other7.4
r_scangle_other6.055
r_dihedral_angle_1_deg5.551
r_scbond_it4.098
r_scbond_other4.098
r_mcangle_it3.778
r_mcangle_other3.778
r_mcbond_it2.744
r_mcbond_other2.74
r_angle_refined_deg1.572
r_angle_other_deg1.476
r_chiral_restr0.088
r_bond_refined_d0.01
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 Atoms5260
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing