X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.9358.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.587α = 90
b = 131.06β = 97.98
c = 72.252γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.655095.10.090.07115.23.553373
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7398.10.580.350.782.23.5

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 REPLACEMENTTHROUGHOUT4FNK2.655050695267695.030.197510.196450.21744RANDOM48.379
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]
0.97-0.360.63-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.078
r_dihedral_angle_4_deg14.776
r_dihedral_angle_3_deg14.676
r_dihedral_angle_1_deg5.936
r_long_range_B_refined4.492
r_long_range_B_other4.482
r_scangle_other2.026
r_angle_refined_deg1.4
r_scbond_it1.206
r_scbond_other1.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.078
r_dihedral_angle_4_deg14.776
r_dihedral_angle_3_deg14.676
r_dihedral_angle_1_deg5.936
r_long_range_B_refined4.492
r_long_range_B_other4.482
r_scangle_other2.026
r_angle_refined_deg1.4
r_scbond_it1.206
r_scbond_other1.206
r_mcangle_it1.072
r_mcangle_other1.072
r_angle_other_deg0.905
r_mcbond_it0.602
r_mcbond_other0.602
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms11526
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms310

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing