7AFV | pdb_00007afv

Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Drop protein volume 0.2 uL Drop well volume 0.1 uL 0.04 M Porpheus Alcohol Mix (Complex ingredient) 0.1 M Morpheus Buffer System 3 pH 8.5 (Buffer) 31 %w/v Morpheus Precipitant Mix 4 (Precipitant) Stock Solutions: Porpheus Alcohol Mix 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol (for a final concentration of 6.7 mM of 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) Morpheus Buffer System 3 pH 8.5 1M Tris and 1M BICINE (for a final concentration of 39.1 mM Bicine pH = 5.03 and 60.9 M Tris pH = 10.83) Morpheus Precipitant Mix 25% w/v PEG 3350, 25% w/v PEG 1000, 25% v/v MPD (for a final concentration of 7.75% w/v PEG 1000, 7.75% w/v PEG 3350 and 7.75% v/v MPD)

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.572	α = 90
b = 87.572	β = 90
c = 56.458	γ = 90

Symmetry
Space Group	P 43 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 PILATUS3 6M		2020-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9795	Diamond	I24

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	2.4	61.92	100	0.999	9.8	23		8519

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53			1.913	0.399	0.789

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	2YXF	2.4	61.92	8519	452	99.77	0.2361	0.2333	0.24	0.2884	0.31	RANDOM	74.502

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]
-1.7			-1.7		3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.399
r_dihedral_angle_4_deg	25.823
r_dihedral_angle_3_deg	17.006
r_mcangle_it	8.652
r_dihedral_angle_1_deg	7.843
r_mcbond_other	5.623
r_mcbond_it	5.621
r_angle_refined_deg	1.553
r_angle_other_deg	1.144
r_chiral_restr	0.051
r_bond_refined_d	0.007
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	1520
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	784

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
xia2	data processing
DIALS	data processing
XSCALE	data reduction
XDS	data reduction
Aimless	data scaling