X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Protein at 20 mg/mL in SD2 plates incubated at 20 C. Crystallisation conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M
Crystal Properties
Matthews coefficientSolvent content
2.4349.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.761α = 90
b = 62.786β = 93.36
c = 120.173γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953716Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.6549.11000.0860.0350.99810.86.8176707
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.681001.2650.5150.6531.57

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 REPLACEMENTTHROUGHOUT6PII1.6549.1167790888599.930.1630.1620.1818RANDOM27.596
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]
-1.49-0.242.11-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.019
r_dihedral_angle_3_deg13.836
r_dihedral_angle_4_deg6.755
r_dihedral_angle_1_deg5.947
r_angle_refined_deg1.604
r_angle_other_deg1.462
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.019
r_dihedral_angle_3_deg13.836
r_dihedral_angle_4_deg6.755
r_dihedral_angle_1_deg5.947
r_angle_refined_deg1.604
r_angle_other_deg1.462
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10048
Nucleic Acid Atoms
Solvent Atoms798
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing