X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.25293Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The ligand was added to the soaking solution at 4 mM concentration. In the soaking drop, Citrate is replaced by Acetate (0.3 M) 150 mM NaCl 0.1 M Bis-Tris pH 6.2 0.3 M Na-Acetate pH 5.2 25% PEG 6K PEG 6K INCREASED to 25% FOR CRYO-PROTECTION
Crystal Properties
Matthews coefficientSolvent content
2.141.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.309α = 90
b = 74.873β = 111.52
c = 67.764γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors (VFM, HFM)2019-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.82656MAX IVBioMAX

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
11.7725.1599.70.08810.16.9455042.117.8
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)
11.771.8194.50.6582.16.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5LBG1.772543132223699.40.1670.1650.214RANDOM29.57
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]
-2.20.85-0.261.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg14.585
r_dihedral_angle_3_deg12.639
r_dihedral_angle_1_deg5.96
r_angle_refined_deg1.699
r_angle_other_deg1.036
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg14.585
r_dihedral_angle_3_deg12.639
r_dihedral_angle_1_deg5.96
r_angle_refined_deg1.699
r_angle_other_deg1.036
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3982
Nucleic Acid Atoms
Solvent Atoms545
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing