X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1M Hepes buffer at pH 7.5, 20% Peg4k, 0.2M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3848.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.361α = 90
b = 85.368β = 107.06
c = 84.804γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.2758.861.50.1138.23.122364
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.272.380.6911.6

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 REPLACEMENTTHROUGHOUT2vx32.32521041105863.380.22190.21870.2851RANDOM40.683
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]
0.16-0.2-0.490.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.109
r_dihedral_angle_4_deg22.494
r_dihedral_angle_3_deg21.156
r_dihedral_angle_1_deg5.654
r_angle_refined_deg1.513
r_angle_other_deg1.215
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.109
r_dihedral_angle_4_deg22.494
r_dihedral_angle_3_deg21.156
r_dihedral_angle_1_deg5.654
r_angle_refined_deg1.513
r_angle_other_deg1.215
r_chiral_restr0.065
r_bond_refined_d0.007
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 Atoms5350
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms57

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction