X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 hexahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9135.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.61α = 90
b = 73.964β = 90
c = 77.115γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.873ESRFID23-1

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
11.634.191000.1616.86.652482
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)
11.61.631000.922.16.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6TGD1.634.1952418259599.9070.1750.17310.209Random23
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]
0.969-1.1240.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.793
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg13.551
r_dihedral_angle_1_deg6.506
r_lrange_it5.551
r_scangle_it4.612
r_scbond_it3.168
r_mcangle_it2.941
r_mcbond_it2.01
r_angle_refined_deg1.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.793
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg13.551
r_dihedral_angle_1_deg6.506
r_lrange_it5.551
r_scangle_it4.612
r_scbond_it3.168
r_mcangle_it2.941
r_mcbond_it2.01
r_angle_refined_deg1.642
r_nbtor_refined0.32
r_nbd_refined0.214
r_symmetry_nbd_refined0.197
r_symmetry_xyhbond_nbd_refined0.155
r_chiral_restr0.104
r_xyhbond_nbd_refined0.104
r_metal_ion_refined0.098
r_gen_planes_refined0.01
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3425
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing