2FC3
Crystal structure of the extremely thermostable Aeropyrum pernix L7Ae multifunctional protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XBI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 20% PEG 4000, 10% Isopropanol, 100 mM HEPES-KOH, pH 7.5, 1 mM ZnCl2 mixed 1:2 with 500 microMolar L7Ae protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.054 | α = 90 |
b = 49.188 | β = 90 |
c = 65.048 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | RIGAKU SATURN 92 | Osmic Confocal Blue Max-Flux | 2004-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
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 | 1.54 | 65.05 | 81.5 | 0.025 | 23.7 | 2.45 | 34157 | 13926 | 3 | 17.53 |
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) | |||||||||||
1 | 1.54 | 1.6 | 15.8 | 0.289 | 2.3 | 1.08 | 1678 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1XBI | 1.56 | 32.44 | 1 | 13760 | 13737 | 695 | 99.08 | 0.177 | 0.177 | 0.174 | 0.19 | 0.226 | 0.23 | RANDOM | 15.807 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.02 | -0.56 | 0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.439 |
r_dihedral_angle_4_deg | 15.801 |
r_sphericity_free | 11.286 |
r_dihedral_angle_3_deg | 11.016 |
r_dihedral_angle_1_deg | 5.482 |
r_scangle_it | 4.634 |
r_scbond_it | 3.161 |
r_sphericity_bonded | 3.042 |
r_rigid_bond_restr | 2.132 |
r_mcangle_it | 1.822 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 957 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data reduction |
CrystalClear | data scaling |