3APW
Crystal structure of the A variant of human alpha1-acid glycoprotein and disopyramide complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3APU | PDB ENTRY 3APU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 30% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 39.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.72 | α = 90 |
b = 45.49 | β = 91.69 |
c = 120.6 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | ADSC QUANTUM 270 | 2009-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.2 | 40.19 | 99.6 | 0.058 | 26.2 | 18846 | 18846 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.2 | 2.32 | 100 | 0.105 | 15.2 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 3APU | 2.2 | 37.76 | 17931 | 915 | 99.45 | 0.23005 | 0.22824 | 0.26339 | RANDOM | 66.109 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.12 | -0.13 | 0.26 | -0.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.092 |
r_dihedral_angle_3_deg | 17.588 |
r_dihedral_angle_4_deg | 14.071 |
r_dihedral_angle_1_deg | 6.082 |
r_scangle_it | 2.531 |
r_scbond_it | 1.533 |
r_angle_refined_deg | 1.291 |
r_mcangle_it | 1.168 |
r_mcbond_it | 0.63 |
r_chiral_restr | 0.098 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2943 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |