8YHF | pdb_00008yhf

The Crystal Structure of the Type I TGF beta receptor from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IAS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.02M K/Na PO4, 0.1M Bis-Tris propane pH6.5, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.86	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.196	α = 90
b = 76.764	β = 90
c = 89.707	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		2022-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	1.4	44.85	96.4	0.999	22	13.1		56084

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	1.4	1.42			0.866

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	1.4	38.757	56025	2711	96.251	0.167	0.1661	0.1924	18.27

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]
-0.403			1.147		-0.744

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.569
r_dihedral_angle_3_deg	11.852
r_dihedral_angle_2_deg	10.52
r_dihedral_angle_1_deg	6.405
r_lrange_it	4.968
r_lrange_other	4.726
r_scangle_it	3.21
r_scangle_other	3.209
r_mcangle_it	2.083
r_mcangle_other	2.082
r_scbond_it	1.978
r_scbond_other	1.977
r_mcbond_it	1.308
r_mcbond_other	1.307
r_angle_refined_deg	1.225
r_angle_other_deg	0.429
r_nbd_refined	0.215
r_nbtor_refined	0.179
r_symmetry_nbd_other	0.178
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.064
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2397
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	30

Software

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