5QSI

PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z933326822

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.1 M SPG pH 7.0, 30 % PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.66	α = 90
b = 99.66	β = 90
c = 99.47	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.54	49.84	100	0.066	0.07	0.023	0.999	13.9	9		28206

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)	Redundancy	Number Unique Reflections (All)
1	1.54	1.58	99.4		1.685	1.836	0.716	0.437		6.4	2057

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6f58	1.64	49.83	22215	1167	99.85	0.1913	0.1889	0.2395	RANDOM	29.652

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]
-0.01	-0.01		-0.01		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.632
r_dihedral_angle_4_deg	18.299
r_dihedral_angle_3_deg	14.822
r_dihedral_angle_1_deg	6.857
r_mcangle_it	3.189
r_mcbond_other	2.12
r_mcbond_it	2.109
r_angle_refined_deg	1.57
r_angle_other_deg	1.347
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.632
r_dihedral_angle_4_deg	18.299
r_dihedral_angle_3_deg	14.822
r_dihedral_angle_1_deg	6.857
r_mcangle_it	3.189
r_mcbond_other	2.12
r_mcbond_it	2.109
r_angle_refined_deg	1.57
r_angle_other_deg	1.347
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1380
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.