X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TO8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M LiCl2, 0.1M Tris pH8.0, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.797α = 90
b = 59.132β = 95.033
c = 67.295γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953732Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.944.38499.80.08413.76.923394
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.701

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.944.38423378114199.7820.1720.16930.229828.469
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]
-1.822-1.2691.8680.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.993
r_dihedral_angle_3_deg14.911
r_dihedral_angle_6_deg14.879
r_dihedral_angle_other_2_deg12.534
r_lrange_it7.719
r_lrange_other7.7
r_scangle_it6.441
r_scangle_other6.439
r_dihedral_angle_1_deg5.777
r_scbond_it4.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.993
r_dihedral_angle_3_deg14.911
r_dihedral_angle_6_deg14.879
r_dihedral_angle_other_2_deg12.534
r_lrange_it7.719
r_lrange_other7.7
r_scangle_it6.441
r_scangle_other6.439
r_dihedral_angle_1_deg5.777
r_scbond_it4.045
r_scbond_other4.044
r_mcangle_other3.636
r_mcangle_it3.634
r_mcbond_it2.68
r_mcbond_other2.674
r_angle_refined_deg1.398
r_angle_other_deg0.48
r_symmetry_nbd_refined0.272
r_nbd_refined0.214
r_nbd_other0.198
r_nbtor_refined0.186
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.166
r_symmetry_xyhbond_nbd_refined0.163
r_symmetry_nbtor_other0.077
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2115
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing