5QRY

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z2856434890


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
2.5451.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.095α = 90
b = 60.095β = 90
c = 110.247γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-23MSINGLE 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
11.5852.781000.0670.070.020.99917.911.828526
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)
11.581.621001.6531.7520.5730.7569.32053

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 SYNTHESISTHROUGHOUT6f581.5852.8227043142099.870.22610.22490.2522RANDOM35.826
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]
1.311.31-2.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.091
r_dihedral_angle_4_deg18.028
r_dihedral_angle_3_deg17.068
r_dihedral_angle_1_deg8.418
r_mcangle_it5.041
r_mcbond_other3.558
r_mcbond_it3.554
r_angle_refined_deg1.876
r_angle_other_deg1.408
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.091
r_dihedral_angle_4_deg18.028
r_dihedral_angle_3_deg17.068
r_dihedral_angle_1_deg8.418
r_mcangle_it5.041
r_mcbond_other3.558
r_mcbond_it3.554
r_angle_refined_deg1.876
r_angle_other_deg1.408
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing