X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DU2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29820 mg/ml in 50 mM sodium acetate (pH4.5) , 40% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.5351.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.298α = 90
b = 132.298β = 90
c = 91.231γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.3345.6698.380.98415.7620167253
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.331.380.659

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 REPLACEMENTTHROUGHOUT2DU21.3345.66167253862298.360.171420.170360.19261RANDOM26.944
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]
-0.82-0.821.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.338
r_long_range_B_refined19.35
r_long_range_B_other19.35
r_dihedral_angle_4_deg17.797
r_dihedral_angle_3_deg14.725
r_dihedral_angle_1_deg6.485
r_scangle_other5.851
r_mcangle_it3.897
r_mcangle_other3.897
r_scbond_it3.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.338
r_long_range_B_refined19.35
r_long_range_B_other19.35
r_dihedral_angle_4_deg17.797
r_dihedral_angle_3_deg14.725
r_dihedral_angle_1_deg6.485
r_scangle_other5.851
r_mcangle_it3.897
r_mcangle_other3.897
r_scbond_it3.832
r_scbond_other3.832
r_mcbond_it2.45
r_mcbond_other2.45
r_angle_refined_deg1.922
r_angle_other_deg1.536
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5547
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing