3NRL
Crystal Structure of protein RUMGNA_01417 from Ruminococcus gnavus, Northeast Structural Genomics Consortium Target UgR76
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Cacodylate Acid (pH 6.5), 18% PEG3350, and 0.2M ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.35 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.581 | α = 90 |
b = 53.072 | β = 90 |
c = 76.477 | 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 | MAR CCD 165 mm | mirrors | 2010-06-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.97915 | NSLS | X4C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.9 | 50 | 98.4 | 0.059 | 0.045 | 29 | 4.3 | 25141 | 24739 | 10.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.9 | 1.93 | 91.2 | 0.365 | 0.301 | 3.1 | 3.7 | 1245 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1.9 | 32.24 | 2 | 1245 | 21676 | 2081 | 86.2 | 0.22 | 0.219 | 0.218 | 0.263 | RANDOM | 30.113 |
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] | |
1.39 | 5.21 | -6.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 9.02 |
c_scbond_it | 6.76 |
c_mcangle_it | 5.12 |
c_mcbond_it | 3.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1140 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |
REFMAC | refinement |