7U68 | pdb_00007u68

Crystal structure of the Vitronectin hemopexin-like domain binding Sodium-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7TXR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION containing 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with 1 mM EDTA, 5 mM SODIUM SULFATE, 27 mM SODIUM NITRATE, 20 mM BisTris pH 7.0, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D-(+)-TREHALOSE.

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.582	α = 90
b = 124.905	β = 119.5
c = 40.778	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 PILATUS 6M		2020-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	35.52	97.6	0.07	9.9	3.5		23279

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	94.8		0.612	2	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7txr	2	35.52	21837	1419	97.45	0.1878	0.1842	0.19	0.247	0.25	RANDOM	32.55

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]
-0.06		0.03	0.12		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.752
r_dihedral_angle_4_deg	18
r_dihedral_angle_3_deg	15.012
r_dihedral_angle_1_deg	7.416
r_angle_refined_deg	1.393
r_angle_other_deg	1.207
r_chiral_restr	0.064
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	3123
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing