6DVU
Structure of the Monoclinic-1 (Monocl-1) Crystal Form of Human Apolipoprotein C1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ROP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | Crystallized in Cryschem sitting drop plates with reservoirs of 16%-18% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were composed of equal amounts of 8 mg/ml protein in 0.02 ammonium bicarbonate and reservoir. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.541 | α = 90 |
b = 46.739 | β = 95.16 |
c = 33.88 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 1992-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 1.8 | 35 | 85.2 | 0.094 | 0.094 | 0.114 | 0.055 | 0.993 | 6.7 | 7.2 | 7315 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.8 | 1.95 | 76 | 0.457 | 0.457 | 0.721 | 0.315 | 0.64 | 3.2 | 4.5 |
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 | 1ROP | 1.8 | 33 | 6965 | 353 | 84.97 | 0.22426 | 0.22139 | 0.27626 | RANDOM | 32.597 |
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] | |
1.91 | -0.49 | -0.02 | -1.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.618 |
r_dihedral_angle_4_deg | 18.166 |
r_dihedral_angle_3_deg | 16.124 |
r_long_range_B_refined | 10.757 |
r_long_range_B_other | 10.754 |
r_scangle_other | 8.977 |
r_scbond_it | 5.896 |
r_scbond_other | 5.89 |
r_mcangle_other | 4.973 |
r_mcangle_it | 4.971 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 859 |
Nucleic Acid Atoms | |
Solvent Atoms | 27 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
UCSD-system | data reduction |
Aimless | data scaling |
PHASER | phasing |