X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M bicine/Trizma base pH 8.5; 0.03 M of each halide; 10% w/v PEG 8000, 20% v/v ethylene glycol B10 Morpheus condition
Crystal Properties
Matthews coefficientSolvent content
3.3863.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.668α = 90
b = 127.025β = 90
c = 130.462γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.69845.8398.30.0560.0650.99913.73.68260633.54
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.895.20.7390.8610.4861.343.63

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 REPLACEMENTTHROUGHOUT5K7Y1.745.8380506210098.310.19160.1910.215RANDOM36.503
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.74
r_dihedral_angle_4_deg13.62
r_dihedral_angle_3_deg12.874
r_dihedral_angle_1_deg6.011
r_angle_other_deg3.613
r_angle_refined_deg1.557
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_other0.013
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.74
r_dihedral_angle_4_deg13.62
r_dihedral_angle_3_deg12.874
r_dihedral_angle_1_deg6.011
r_angle_other_deg3.613
r_angle_refined_deg1.557
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_other0.013
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3831
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Cootmodel building