X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Z68 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30 % (w/v) PEG 4000, 2 mM methyl 4-methylumbelliferyl hexylphosphat
Crystal Properties
Matthews coefficientSolvent content
2.1342.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.41α = 90
b = 86.7β = 90
c = 110.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9762ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8143.3998.930.1170.99610.34.963348
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)
11.8111.8750.5550.82

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 REPLACEMENTTHROUGHOUT6Z681.8143.3959945315298.930.1530.15090.1922RANDOM15.82
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]
-0.310.55-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.424
r_dihedral_angle_4_deg18.474
r_dihedral_angle_3_deg13.541
r_dihedral_angle_1_deg6.094
r_angle_refined_deg1.648
r_angle_other_deg1.442
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.424
r_dihedral_angle_4_deg18.474
r_dihedral_angle_3_deg13.541
r_dihedral_angle_1_deg6.094
r_angle_refined_deg1.648
r_angle_other_deg1.442
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5436
Nucleic Acid Atoms
Solvent Atoms962
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
XDSdata reduction