X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5277KSCN, NaBr, PEG 6000, PEG 8000, PEG 10000
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.92α = 90
b = 82.433β = 110.77
c = 42.608γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.641.2297.90.0510.0610.0330.99814.23.431598
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)
11.61.6397.90.4190.4960.2630.83.5

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 REPLACEMENTTHROUGHOUT4NYX1.641.2230091148397.760.16340.16240.1854RANDOM20.09
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]
0.990.1-0.84-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.329
r_dihedral_angle_4_deg17.256
r_dihedral_angle_3_deg11.802
r_dihedral_angle_1_deg4.883
r_angle_refined_deg1.353
r_angle_other_deg0.904
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.329
r_dihedral_angle_4_deg17.256
r_dihedral_angle_3_deg11.802
r_dihedral_angle_1_deg4.883
r_angle_refined_deg1.353
r_angle_other_deg0.904
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1943
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms74

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction