X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NB4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 M Potassium sodium tartrate, 20% (W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.59α = 78.37
b = 108.63β = 82.53
c = 116.93γ = 62.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARRESEARCH2019-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.979RRCAT INDUS-2PX-BL21

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
12.2142.1797.30.99715.63.9225119
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)
12.212.210.974

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 REPLACEMENTTHROUGHOUT5NB42.2142.172140131110397.230.16540.16310.2101RANDOM17.951
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]
-0.31-0.12-0.16-0.65-0.161.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.966
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg14.388
r_dihedral_angle_1_deg5.961
r_angle_refined_deg1.575
r_angle_other_deg1.375
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.966
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg14.388
r_dihedral_angle_1_deg5.961
r_angle_refined_deg1.575
r_angle_other_deg1.375
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31086
Nucleic Acid Atoms
Solvent Atoms2776
Heterogen Atoms2580

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing