6V7M | pdb_00006v7m

Crystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NFN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	298	Crystallization was by sitting drop vapor diffusion in Cryschem plates at room temperature. Reservoirs were 16% to 18 % 2-methyl-2,4-pentanediol (MPD) buffered with 0.1 M sodium acetate at pH 5.8 and including 0.25% octyl-beta-D-1-thioglucopyranoside. The droplets were initial composed of equal amounts of the reservoir and an 8 mg/ml solution of the protein in 0.02 M ammonium carbonate.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.33	α = 90
b = 54.45	β = 90
c = 86.67	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	298	AREA DETECTOR	SDMS		1993-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	46.33	86	0.241	0.24	0.277	0.127	0.968	3.9	3.8		11748			28

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	2.01	2.06			0.528	0.747	0.528	0.096	1.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1NFN	2	46	10817	572	82.88	0.2054	0.2025	0.2598	RANDOM	49.084

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]
1.74			-1.92		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.882
r_dihedral_angle_4_deg	18.707
r_dihedral_angle_3_deg	15.759
r_dihedral_angle_1_deg	5.157
r_angle_refined_deg	1.287
r_angle_other_deg	1.208
r_chiral_restr	0.054
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.882
r_dihedral_angle_4_deg	18.707
r_dihedral_angle_3_deg	15.759
r_dihedral_angle_1_deg	5.157
r_angle_refined_deg	1.287
r_angle_other_deg	1.208
r_chiral_restr	0.054
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1205
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	5

Software

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

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 R01GM157729.