9F6X | pdb_00009f6x

Human transforming growth factor b type I receptor in complex with kinase inhibitor SB505124

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	5.6	291	23%(w/v) PEG 3350, 3%(v/v) glycerol at pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.07	α = 90
b = 79.846	β = 90
c = 87.8	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 EIGER2 R 1M		2022-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87	ESRF	ID30B

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	1.9	59.07	100	0.997	8.2	15		12847

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	2.68	2.74	99.2		0.36

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.68	10.87	8038	404	96.24	0.21399	0.21223	0.2176	0.2477	0.2577	RANDOM	40.776

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]
-0.09			0.87		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.41
r_dihedral_angle_3_deg	14.477
r_dihedral_angle_1_deg	10.844
r_long_range_B_refined	4.686
r_long_range_B_other	4.621
r_angle_refined_deg	2.241
r_mcangle_it	1.23
r_mcangle_other	1.23
r_angle_other_deg	1.195
r_scangle_other	1.142
r_mcbond_it	0.674
r_mcbond_other	0.674
r_scbond_it	0.648
r_scbond_other	0.648
r_chiral_restr	0.116
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2425
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
REFMAC	phasing