8YGZ | pdb_00008ygz

The Crystal Structure of TGF beta R2 kinase domain from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E8V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 30% PEG4,000

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.09	α = 90
b = 75.02	β = 90
c = 77.704	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2021-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18064	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	48.03	100	0.999	19.4	6.4		21483

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.752

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	48.03	21432	1025	99.944	0.198	0.1949	0.2	0.254	0.26	44.21

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]
1.145			0.344		-1.488

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.482
r_dihedral_angle_3_deg	14.735
r_dihedral_angle_4_deg	12.892
r_lrange_it	7.679
r_lrange_other	7.667
r_dihedral_angle_1_deg	7.254
r_scangle_it	5.943
r_scangle_other	5.942
r_mcangle_it	4.982
r_mcangle_other	4.981
r_scbond_it	3.998
r_scbond_other	3.997
r_mcbond_it	3.528
r_mcbond_other	3.522
r_angle_refined_deg	1.443
r_angle_other_deg	1.263
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.171
r_nbd_other	0.167
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.152
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
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	2310
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing