X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6MGP6MGP, 4XTA
experimental modelPDB 4XTA6MGP, 4XTA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52911.5 M lithium sulfate, 100 mM Tris (pH 8.5), 10 mM nickel sulfate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.851α = 90
b = 106.851β = 90
c = 146.41γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2020-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

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
13.1447.7999.90.1620.0470.99816.112.915429
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)
13.143.3699.81.2410.3590.89412.8

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 REPLACEMENTTHROUGHOUT6MGP, 4XTA3.1447.791465472699.880.21360.21130.2581RANDOM90.054
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]
4.124.12-8.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.381
r_dihedral_angle_4_deg21.843
r_dihedral_angle_3_deg19.981
r_dihedral_angle_1_deg9.261
r_angle_refined_deg2.142
r_angle_other_deg1.555
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.381
r_dihedral_angle_4_deg21.843
r_dihedral_angle_3_deg19.981
r_dihedral_angle_1_deg9.261
r_angle_refined_deg2.142
r_angle_other_deg1.555
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1994
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing