5QSG

PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z2856434903


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72980.1 M SPG pH 7.0, 30 % PEG 1000
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.68α = 90
b = 99.68β = 90
c = 99.618γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-12-09MSINGLE 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
11.8749.841000.2270.240.0770.995.29.615933
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)
11.871.921001.3481.4210.4470.9019.91162

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 SYNTHESISTHROUGHOUT6f581.8749.841473379797.330.22810.22560.2729RANDOM30.258
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]
-0.91-0.45-0.912.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.295
r_dihedral_angle_3_deg15.903
r_dihedral_angle_4_deg13.472
r_dihedral_angle_1_deg7.535
r_mcangle_it3.228
r_mcbond_other2.059
r_mcbond_it2.056
r_angle_refined_deg1.595
r_angle_other_deg1.259
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.295
r_dihedral_angle_3_deg15.903
r_dihedral_angle_4_deg13.472
r_dihedral_angle_1_deg7.535
r_mcangle_it3.228
r_mcbond_other2.059
r_mcbond_it2.056
r_angle_refined_deg1.595
r_angle_other_deg1.259
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1380
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing