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
2.9658.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.344α = 90
b = 131.41β = 98.65
c = 72.345γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0331APS23-ID-D

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
12.255099.90.080.03117.86.691825
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3299.30.60.271.85.6

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 REPLACEMENTTHROUGHOUT4FNK2.255087261456399.410.18180.180450.20765RANDOM55.453
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]
0.96-0.850.13-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.548
r_dihedral_angle_4_deg15.572
r_dihedral_angle_3_deg13.741
r_dihedral_angle_1_deg5.893
r_long_range_B_refined4.857
r_long_range_B_other4.771
r_scangle_other2.295
r_scbond_it1.399
r_scbond_other1.399
r_angle_refined_deg1.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.548
r_dihedral_angle_4_deg15.572
r_dihedral_angle_3_deg13.741
r_dihedral_angle_1_deg5.893
r_long_range_B_refined4.857
r_long_range_B_other4.771
r_scangle_other2.295
r_scbond_it1.399
r_scbond_other1.399
r_angle_refined_deg1.371
r_mcangle_it1.34
r_mcangle_other1.34
r_angle_other_deg1.124
r_mcbond_it0.802
r_mcbond_other0.802
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms685
Heterogen Atoms364

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing