9GH7 | pdb_00009gh7

Complex of human TfR1 with a potent bicyclic peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In-house generated Apo model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M ammonium tartrate dibasic pH 7.0, 12% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.955	α = 90
b = 94.955	β = 90
c = 225.997	γ = 90

Symmetry
Space Group	P 41 21 2

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 XE 16M	80x20	2021-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.079	87.542	95.7	0.078	0.08	0.016	1	23.1	24.8		48208

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.079	2.264	75.8		1.256	1.308	0.363	0.769	1.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.079	87.542	48208	2438	76.422	0.2	0.1983	0.2076	0.2351	0.235	Random selection	52.518

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]
-0.079			-0.079		0.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.938
r_dihedral_angle_6_deg	14.52
r_lrange_it	8.931
r_lrange_other	8.931
r_scangle_it	7.537
r_scangle_other	7.536
r_dihedral_angle_1_deg	7.322
r_dihedral_angle_2_deg	6.472
r_mcangle_it	5.83
r_mcangle_other	5.829
r_scbond_it	5.24
r_scbond_other	5.239
r_mcbond_it	4.26
r_mcbond_other	4.26
r_dihedral_angle_other_3_deg	2.117
r_angle_refined_deg	1.722
r_angle_other_deg	0.596
r_nbd_refined	0.225
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.181
r_xyhbond_nbd_refined	0.172
r_nbd_other	0.167
r_symmetry_nbd_refined	0.154
r_metal_ion_refined	0.14
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.007
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	5098
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	78

Software

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