9R5Y | pdb_00009r5y

Crystal structure of the C-terminal domain of human TNC in complex with Adhiron 52

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	291.15	10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.535	α = 90
b = 90.152	β = 90
c = 104.409	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 XE 16M		2019-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.980	Diamond	I04

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	1.399	58.854	99.61	0.999	15.8	12.6		143762			13.5

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	1.399	1.436			0.823	0.884	0.313	0.825	1.8

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	1.399	58.854	143762	7047	99.617	0.162	0.1608	0.1604	0.185	0.1846	21.037

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]
0.565			0.076		-0.641

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.744
r_dihedral_angle_4_deg	16.711
r_dihedral_angle_3_deg	11.026
r_dihedral_angle_1_deg	7.233
r_lrange_it	2.585
r_lrange_other	2.521
r_scangle_it	2.094
r_scangle_other	2.094
r_mcangle_it	1.867
r_mcangle_other	1.867
r_scbond_it	1.656
r_scbond_other	1.656
r_mcbond_it	1.475
r_mcbond_other	1.474
r_angle_other_deg	1.365
r_angle_refined_deg	1.295
r_rigid_bond_restr	0.906
r_nbd_refined	0.19
r_nbd_other	0.189
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.102
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbd_refined	0.08
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	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	4605
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms

Software

Software
Software Name	Purpose
xia2	data reduction
PHASER	phasing
Coot	model building
REFMAC	refinement