X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6IU5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729321-23% PEG600, 0.1 M HEPES pH7.0 and 0.001-0.003 M zinc cloride
Crystal Properties
Matthews coefficientSolvent content
2.7755.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.744α = 90
b = 84.744β = 90
c = 97.398γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.485SPring-8BL41XU

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
12.942.37299.98850.12590.140.0610.99187.75055.117355
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)
12.93.003999.8870.3060.8874.9949

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 REPLACEMENTTHROUGHOUT6IU52.942.371655779899.970.14770.14480.2113RANDOM66.441
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]
5.475.47-10.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.689
r_dihedral_angle_4_deg22.151
r_dihedral_angle_3_deg18.89
r_dihedral_angle_1_deg6.559
r_angle_refined_deg1.754
r_angle_other_deg1.32
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.689
r_dihedral_angle_4_deg22.151
r_dihedral_angle_3_deg18.89
r_dihedral_angle_1_deg6.559
r_angle_refined_deg1.754
r_angle_other_deg1.32
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4716
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing