5QRT | pdb_00005qrt

PanDDA analysis group deposition -- Crystal Structure of human Brachyury in complex with Z31735562

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F58	6f58

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
2.53	51.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.95	α = 90
b = 59.95	β = 90
c = 110.32	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		2018-07-22	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	1.77	52.67	99.7	0.077	0.081	0.023	0.999	16.7	12.6		20302

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	1.77	1.82	99.7		3.217	3.345	0.906	0.58		13.3	1456

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6f58	1.77	52.73	19288	975	99.62	0.2221	0.2201	0.2384	0.2649	0.2747	RANDOM	44.043

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]
1.61			1.61		-3.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.847
r_dihedral_angle_3_deg	17.413
r_dihedral_angle_4_deg	9.322
r_dihedral_angle_1_deg	7.724
r_mcangle_it	5.691
r_mcbond_it	3.83
r_mcbond_other	3.809
r_angle_refined_deg	1.543
r_angle_other_deg	1.311
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	20

Software

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