X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M lithium citrate, 0.1 M MES-NaOH pH 6.5 and 20% PEG4000
Crystal Properties
Matthews coefficientSolvent content
3.1260.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.587α = 90
b = 112.587β = 90
c = 212.11γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2019-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B10.99999SPring-8BL26B1

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
12.63948.7599.80.1120.1180.0360.99917.819.3241561
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)
12.642.772.8212.9630.9020.73519.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2VPV2.63947.55824086117099.760.1880.1850.251797.076
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]
0.0750.0370.075-0.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.924
r_dihedral_angle_4_deg18.646
r_dihedral_angle_3_deg16.713
r_lrange_it10.802
r_scangle_it10.111
r_scbond_it8.406
r_mcangle_it8.338
r_dihedral_angle_1_deg7.702
r_mcbond_it6.291
r_rigid_bond_restr2.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.924
r_dihedral_angle_4_deg18.646
r_dihedral_angle_3_deg16.713
r_lrange_it10.802
r_scangle_it10.111
r_scbond_it8.406
r_mcangle_it8.338
r_dihedral_angle_1_deg7.702
r_mcbond_it6.291
r_rigid_bond_restr2.919
r_angle_refined_deg1.236
r_nbtor_refined0.306
r_nbd_refined0.22
r_symmetry_nbd_refined0.204
r_xyhbond_nbd_refined0.121
r_symmetry_xyhbond_nbd_refined0.115
r_chiral_restr0.086
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3046
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
BUCCANEERphasing