5QS2

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z291279160


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52980.1 M CdCl, 0.1 M Acetate pH 4.5, 32% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.5551.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.29α = 90
b = 60.29β = 90
c = 110.02γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6855.0199.80.1110.1160.0330.99712.612.723883
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7299.52.4642.5710.7290.64712.31721

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6f581.6852.9322670116599.720.22250.22140.2439RANDOM37.885
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]
1.221.22-2.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.006
r_dihedral_angle_4_deg21.404
r_dihedral_angle_3_deg20.158
r_dihedral_angle_1_deg7.621
r_mcangle_it4.988
r_mcbond_other3.072
r_mcbond_it3.069
r_angle_refined_deg1.638
r_angle_other_deg1.329
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.006
r_dihedral_angle_4_deg21.404
r_dihedral_angle_3_deg20.158
r_dihedral_angle_1_deg7.621
r_mcangle_it4.988
r_mcbond_other3.072
r_mcbond_it3.069
r_angle_refined_deg1.638
r_angle_other_deg1.329
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1369
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing