3FYD
Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QYR | composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 |
experimental model | PDB | 2H1R | composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 |
experimental model | PDB | 1ZQ9 | composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | PEG 8000 (14-16%), 25 mM MES, 50 MM NH2SO4, 7 mM MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.236 | α = 90 |
b = 65.906 | β = 108.1 |
c = 61.932 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | Rigaku Varimax Confocal Optics | 2008-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.75 | 33.1 | 94.4 | 0.038 | 29.1 | 7.06 | 31119 | 29365 | 38.9 |
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) | |||||||||||
1.75 | 1.81 | 91.1 | 0.294 | 4.9 | 6.98 | 3079 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 | 1.75 | 22 | 31106 | 26413 | 2926 | 94.37 | 0.18126 | 0.17624 | 0.22643 | RANDOM | 43.95 |
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] | |
-0.07 | -0.42 | -0.48 | 0.3 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_2_deg | 32.708 |
f_dihedral_angle_4_deg | 14.768 |
f_dihedral_angle_3_deg | 14.475 |
f_scangle_it | 9.584 |
f_scbond_it | 8.044 |
f_dihedral_angle_1_deg | 5.679 |
f_mcangle_it | 4.87 |
f_mcbond_it | 4.041 |
f_angle_refined_deg | 1.133 |
f_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2177 |
Nucleic Acid Atoms | |
Solvent Atoms | 333 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
PHENIX | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |