2GAB
Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-3,3',5,4'-tetrachlorobiphenyl
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BMZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | CRYSTALLIZATION CONDITIONS: CRYSTALS OF RECOMBINANT WT TTR WERE OBTAINED FROM PROTEIN SOLUTIONS AT 5 MG/ML (IN 100 MM KCL, 100 MM PHOSPHATE [PH 7.4], 1 M AMMONIUM SULFATE) EQUILIBRATED AGAINST 2 M AMMONIUM SULFATE IN HANGING DROP EXPERIMENTS. THE TTR LIGAND COMPLEXES WERE PREPARED FROM CRYSTALS SOAKED FOR 2 WEEKS WITH A 10-FOLD MOLAR EXCESS , PH 7.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K , VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.459 | α = 90 |
b = 86.197 | β = 90 |
c = 65.488 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 120 | IMAGE PLATE | MAC Science DIP-2030 | 1999-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 1.85 | 65.51 | 89.2 | 0.03 | 19133 | 19133 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.8 | 1.86 | 92.35 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1BMZ | 1.85 | 65.51 | 19133 | 18145 | 988 | 88.22 | 0.21147 | 0.21147 | 0.21008 | 0.23769 | RANDOM | 23.974 |
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 | 0.03 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.822 |
r_dihedral_angle_4_deg | 26.403 |
r_dihedral_angle_3_deg | 14.456 |
r_dihedral_angle_1_deg | 5.676 |
r_scangle_it | 5.293 |
r_scbond_it | 3.26 |
r_angle_refined_deg | 2.272 |
r_mcangle_it | 2.105 |
r_mcbond_it | 1.101 |
r_nbtor_refined | 0.311 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1731 |
Nucleic Acid Atoms | |
Solvent Atoms | 75 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |