X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JDS5JDS, 5M2J
experimental modelPDB 5M2J5JDS, 5M2J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.62α = 90
b = 97.99β = 90.02
c = 67.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.978SSRFBL19U1

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
11.6439.6594.60.0410.0310.999153.551992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.6792.60.4410.796

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 REPLACEMENTTHROUGHOUT5JDS, 5M2J1.6439.6549377258694.360.15130.14960.1837RANDOM19.532
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]
9.655.88-9.61-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.693
r_dihedral_angle_4_deg17.961
r_dihedral_angle_3_deg11.83
r_dihedral_angle_1_deg7.391
r_angle_refined_deg1.244
r_angle_other_deg1.221
r_chiral_restr0.051
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.693
r_dihedral_angle_4_deg17.961
r_dihedral_angle_3_deg11.83
r_dihedral_angle_1_deg7.391
r_angle_refined_deg1.244
r_angle_other_deg1.221
r_chiral_restr0.051
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3650
Nucleic Acid Atoms
Solvent Atoms586
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing