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
1.294.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.781α = 90
b = 132.781β = 90
c = 92.07γ = 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
11.3846.9999.370.9611.6516.6155462
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)
11.381.4290.56

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 REPLACEMENTTHROUGHOUT2DU21.3846.99155462824299.090.197180.195830.22361RANDOM23.001
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]
-0.04-0.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.369
r_dihedral_angle_3_deg13.813
r_dihedral_angle_4_deg11.492
r_long_range_B_refined10.93
r_long_range_B_other10.656
r_dihedral_angle_1_deg8.031
r_scangle_other4.608
r_mcangle_it4.289
r_mcangle_other4.288
r_scbond_it3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.369
r_dihedral_angle_3_deg13.813
r_dihedral_angle_4_deg11.492
r_long_range_B_refined10.93
r_long_range_B_other10.656
r_dihedral_angle_1_deg8.031
r_scangle_other4.608
r_mcangle_it4.289
r_mcangle_other4.288
r_scbond_it3
r_scbond_other3
r_mcbond_it2.783
r_mcbond_other2.783
r_angle_refined_deg1.848
r_angle_other_deg1.538
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5682
Nucleic Acid Atoms
Solvent Atoms740
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing