5QSK | pdb_00005qsk

PanDDA analysis group deposition -- Crystal Structure of human Brachyury G177D variant in complex with Z2856434906

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
2.41	48.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.444	α = 90
b = 99.444	β = 90
c = 99.542	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	1.55	65.12	100	0.042	0.045	0.015	0.999	20.6	8.9		27580

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	1.55	1.59	100		1.444	1.577	0.626	0.612		6.2	2007

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	1.55	65.13	26162	1387	99.83	0.1951	0.1941	0.22	0.2135	0.24	RANDOM	29.566

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]
-0.87	-0.43		-0.87		2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.648
r_dihedral_angle_3_deg	15.948
r_dihedral_angle_4_deg	15.513
r_dihedral_angle_1_deg	7.225
r_mcangle_it	3.817
r_mcbond_it	2.48
r_mcbond_other	2.469
r_angle_refined_deg	1.621
r_angle_other_deg	1.365
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.648
r_dihedral_angle_3_deg	15.948
r_dihedral_angle_4_deg	15.513
r_dihedral_angle_1_deg	7.225
r_mcangle_it	3.817
r_mcbond_it	2.48
r_mcbond_other	2.469
r_angle_refined_deg	1.621
r_angle_other_deg	1.365
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1380
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	12

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.