8R21 | pdb_00008r21

Alpha-1-antitrypsin (Ile340Trp) in the native conformation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I7U	Alpha-1-antitrypsin variant

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	293	0.1M SPG (succinate-phosphate-glycine) pH 5.25, 17.5% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.45	α = 90
b = 113.45	β = 90
c = 136.743	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 EIGER X 16M	Compound refractive lenses	2018-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	2.878	98.251	81.2	0.213	0.223	0.067	0.997	9.8	10.7		19154			69.45

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	2.878	3.071			2.298	2.4	0.684	0.42	1.3	12.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.88	98.25	1.34	19148	876	81.19	0.1994	0.1974	0.2	0.2422	0.2431	74.35

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.9038
f_angle_d	0.4692
f_chiral_restr	0.0402
f_plane_restr	0.0033
f_bond_d	0.0022

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5412
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
STARANISO	data scaling
Aimless	data scaling
XDS	data reduction
PHASER	phasing