X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6DK2PDB entry 6DK2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293Molecular Dimensions Crystal Strategy Screen I, well G3 (0.2 M magnesium chloride, 0.1 M Tris acetate, pH 8.5, 25% PEG2000 MME).
Crystal Properties
Matthews coefficientSolvent content
3.1961.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 228.845α = 90
b = 228.845β = 90
c = 246.517γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

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
12.449.699.930.22490.23960.9968.48.5283596
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.48799.521.7550.581.117.3

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 REPLACEMENTTHROUGHOUTPDB entry 6DK22.449.62694561414099.870.19220.18960.2423RANDOM34.414
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]
-1.49-0.74-1.494.83
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free70.055
r_dihedral_angle_2_deg35.698
r_sphericity_bonded31.192
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg15.77
r_dihedral_angle_1_deg6.323
r_rigid_bond_restr3.612
r_angle_refined_deg0.996
r_angle_other_deg0.812
r_chiral_restr0.047
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free70.055
r_dihedral_angle_2_deg35.698
r_sphericity_bonded31.192
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg15.77
r_dihedral_angle_1_deg6.323
r_rigid_bond_restr3.612
r_angle_refined_deg0.996
r_angle_other_deg0.812
r_chiral_restr0.047
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms40685
Nucleic Acid Atoms
Solvent Atoms944
Heterogen Atoms812

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction