6V7M
Crystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.3 | 46.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.33 | α = 90 |
b = 54.45 | β = 90 |
c = 86.67 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR571 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | 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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1205 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SDMS | data reduction |
Aimless | data scaling |
PHASER | phasing |