X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Bis-Tris pH 5.5, 2.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.8857.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.197α = 90
b = 94.197β = 90
c = 189.003γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS EIGER X 16M2018-10-23MSINGLE 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
11.4247.1299.70.99510.410.1181988
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)
11.421.470.876

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 REPLACEMENTTHROUGHOUT5YOT1.4229.48172870909999.70.11950.1180.1469RANDOM20.214
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]
0.10.050.1-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_4_deg15.116
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.757
r_rigid_bond_restr4.6
r_angle_refined_deg2.11
r_angle_other_deg1.664
r_chiral_restr0.128
r_bond_refined_d0.017
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.853
r_dihedral_angle_4_deg15.116
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg6.757
r_rigid_bond_restr4.6
r_angle_refined_deg2.11
r_angle_other_deg1.664
r_chiral_restr0.128
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5836
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing