3CYG
Crystal structure of an uncharacterized protein from Fervidobacterium nodosum Rt17-B1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 300 | 25% PEG 3500, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 49.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.228 | α = 90 |
b = 72.794 | β = 90 |
c = 166.359 | 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 | ADSC QUANTUM 315 | Mirrors | 2008-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9791 | NSLS | X29A |
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 | 2.61 | 50 | 94.4 | 0.074 | 11.9 | 12.2 | 15697 | 15697 | 68.5 |
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) | |||||||||||
2.61 | 2.69 | 54.8 | 0.25 | 1 | 5.7 | 883 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.61 | 36.53 | 15697 | 14982 | 746 | 91.8 | 0.29 | 0.244 | 0.244 | 0.299 | RANDOM | 59.1 |
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] | |
9.55 | 5.58 | -15.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.9 |
c_scangle_it | 3.26 |
c_mcangle_it | 2.73 |
c_scbond_it | 2.08 |
c_mcbond_it | 1.55 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.86 |
c_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3403 |
Nucleic Acid Atoms | |
Solvent Atoms | 69 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CBASS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELXD | phasing |
SHARP | phasing |
ARP/wARP | model building |