X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5US4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.32933.0 % Xylitol, 0.2 M ammonium acetate and 2.2 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.448.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.93α = 90
b = 84.93β = 90
c = 89.3γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.8444.651000.1190.1290.99410.096.896203135.229
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.951000.5550.6020.7792.697.04

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 REPLACEMENTTHROUGHOUT5US41.8444.6559030299599.040.13450.13330.158RANDOM30.044
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]
-7.66-7.6615.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.349
r_dihedral_angle_4_deg17.247
r_dihedral_angle_3_deg12.572
r_dihedral_angle_1_deg5.939
r_angle_refined_deg1.561
r_angle_other_deg1.283
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.349
r_dihedral_angle_4_deg17.247
r_dihedral_angle_3_deg12.572
r_dihedral_angle_1_deg5.939
r_angle_refined_deg1.561
r_angle_other_deg1.283
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5340
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms132

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing