4IB4
Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PBL | PDB Entry 3PBL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Lipid Cubic Phase (LCP) | 8 | 293 | 100 mM Tris/HCl pH 8.0, 100 mM magnesium sulfate and 30% (v/v) PEG400, Lipid Cubic Phase (LCP) , temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.571 | α = 90 |
b = 119.75 | β = 90 |
c = 170.607 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 100 | CCD | MARMOSAIC 300 mm CCD | mirrors | 2012-08-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0330 | APS | 23-ID-D |
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 | 2.7 | 50 | 90.5 | 0.15 | 8.7 | 3.2 | 16041 | 72.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 2.7 | 2.8 | 92.2 | 0.91 | 1.7 | 3.1 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 3PBL | 2.7 | 24.84 | 15818 | 823 | 90.69 | 0.2265 | 0.2244 | 0.2663 | RANDOM | 80.04 |
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] | |
-2.0121 | -1.2375 | 3.2497 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_other_torsion | 3.09 |
f_omega_torsion | 1.91 |
f_angle_deg | 0.99 |
f_bond_d | 0.009 |
f_dihedral_angle_d | |
f_incorr_chiral_ct | |
f_pseud_angle | |
f_trig_c_planes | |
f_gen_planes | |
f_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2849 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 205 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
PHENIX | refinement |
BUSTER | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |