5QRF

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z373768900

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1 M CdCl, 0.1 M Acetate pH 4.5, 32% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.06	α = 90
b = 60.06	β = 90
c = 110.25	γ = 90

Symmetry
Space Group	P 41 2 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		2018-07-15	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	2.03	40.61	100	0.126	0.132	0.037	0.999	12.9	12.5		13712

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	2.03	2.08	99.9		1.75	1.822	0.504	0.803		12.9	990

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	2.03	40.65	13017	656	99.91	0.2126	0.2097	0.2756	RANDOM	48.094

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]
1.62			1.62		-3.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.101
r_dihedral_angle_3_deg	16.891
r_dihedral_angle_4_deg	15.434
r_dihedral_angle_1_deg	7.14
r_mcangle_it	5.949
r_mcbond_it	3.822
r_mcbond_other	3.819
r_angle_refined_deg	1.506
r_angle_other_deg	1.271
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.101
r_dihedral_angle_3_deg	16.891
r_dihedral_angle_4_deg	15.434
r_dihedral_angle_1_deg	7.14
r_mcangle_it	5.949
r_mcbond_it	3.822
r_mcbond_other	3.819
r_angle_refined_deg	1.506
r_angle_other_deg	1.271
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	18

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 R01GM133198.