5QRG

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z275151340

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
2.51	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.74	α = 90
b = 59.74	β = 90
c = 110.35	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	1.95	59.74	99.6	0.157	0.164	0.047	0.997	10.5	12.4		15203

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	1.95	2	99.5		2.485	2.583	0.701	0.689		13.2	1098

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	1.95	59.74	14451	726	99.48	0.2211	0.2184	0.2814	RANDOM	43.69

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]
1.44			1.44		-2.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.472
r_dihedral_angle_3_deg	16.801
r_dihedral_angle_4_deg	14.423
r_dihedral_angle_1_deg	7.528
r_mcangle_it	6.087
r_mcbond_it	3.874
r_mcbond_other	3.872
r_angle_refined_deg	1.554
r_angle_other_deg	1.257
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.472
r_dihedral_angle_3_deg	16.801
r_dihedral_angle_4_deg	14.423
r_dihedral_angle_1_deg	7.528
r_mcangle_it	6.087
r_mcbond_it	3.874
r_mcbond_other	3.872
r_angle_refined_deg	1.554
r_angle_other_deg	1.257
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	19

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.