8YHL | pdb_00008yhl

The Crystal Structure of Tgf-Beta Type I Receptor (Alk5) from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WOT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MgAC2, 0.1M MES pH6.5, 10% PEG10,000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.813	α = 90
b = 77.464	β = 90
c = 89.524	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		2022-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18067	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	1.47	44.76	100	0.999	18.3	6.4		50369

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	1.47	1.5			0.683

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.47	38.762	50302	2460	99.96	0.165	0.1634	0.1932	18.485

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]
-0.353			0.288		0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.231
r_dihedral_angle_4_deg	15.263
r_dihedral_angle_3_deg	10.322
r_dihedral_angle_1_deg	6.805
r_lrange_it	5.325
r_lrange_other	5.149
r_scangle_it	3.827
r_scangle_other	3.826
r_scbond_it	2.517
r_scbond_other	2.516
r_mcangle_other	2.08
r_mcangle_it	2.078
r_angle_refined_deg	1.726
r_mcbond_it	1.554
r_mcbond_other	1.491
r_angle_other_deg	1.485
r_nbd_refined	0.22
r_nbd_other	0.216
r_xyhbond_nbd_refined	0.202
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.125
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2433
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	46

Software

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