8S6Y | pdb_00008s6y

Co-crystal structure of TEAD1 with OPN-9652

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		IN HOUSE MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	buffer, salt and precipitant

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.957	α = 90
b = 120.957	β = 90
c = 155.52	γ = 120

Symmetry
Space Group	P 32 2 1

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 X CdTe 16M		2024-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885603	ESRF	ID23-1

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	2.031	104.752	95.4	0.99	6.5	12.6		81249

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	2.031	2.066			0.664

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	2.031	104.752	81103	647	95.156	0.224	0.2233	0.2258	0.2581	0.2625	39.692

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]
0.609	0.304		0.609		-1.975

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.784
r_dihedral_angle_4_deg	13.153
r_dihedral_angle_3_deg	11.767
r_dihedral_angle_1_deg	7.146
r_lrange_it	5.894
r_lrange_other	5.832
r_dihedral_angle_other_3_deg	4.424
r_mcangle_other	3.153
r_mcangle_it	3.152
r_scangle_it	2.732
r_scangle_other	2.731
r_mcbond_it	1.787
r_mcbond_other	1.787
r_scbond_it	1.575
r_scbond_other	1.575
r_angle_refined_deg	1.336
r_angle_other_deg	1.099
r_nbtor_refined	0.149
r_nbd_refined	0.144
r_symmetry_nbd_other	0.144
r_symmetry_nbd_refined	0.138
r_nbd_other	0.13
r_xyhbond_nbd_refined	0.11
r_symmetry_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.065
r_ncsr_local_group_2	0.05
r_chiral_restr	0.046
r_ncsr_local_group_3	0.046
r_ncsr_local_group_1	0.045
r_ncsr_local_group_5	0.044
r_ncsr_local_group_6	0.043
r_ncsr_local_group_4	0.042
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6959
Nucleic Acid Atoms
Solvent Atoms	591
Heterogen Atoms	276

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing