7F2R

Crystal structure of VinK-VinL covalent complex formed with a pantetheineamide cross-linking probe

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	PEG8000, magnesium chloride, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.282	α = 90
b = 148.224	β = 91.08
c = 68.791	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2021-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.95	50	99	0.047	0.065	0.998	9.3	3.3		63757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	99.9		0.332	0.462	0.896	2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5CZD	1.95	40.16	60569	3149	98.96	0.1957	0.1933	0.2414	RANDOM	33.219

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]
-0.68		1.66	-0.38		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.911
r_dihedral_angle_4_deg	13.124
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_1_deg	6.756
r_angle_refined_deg	1.849
r_angle_other_deg	1.617
r_chiral_restr	0.156
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.911
r_dihedral_angle_4_deg	13.124
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_1_deg	6.756
r_angle_refined_deg	1.849
r_angle_other_deg	1.617
r_chiral_restr	0.156
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6004
Nucleic Acid Atoms
Solvent Atoms	689
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.