1R6Y
Crystal structure of YgiN from Escherichia coli
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 295 | Ammonium Sulphate, Tri-Sodium Citrate, Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.43 | 64.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.057 | α = 90 |
b = 102.057 | β = 90 |
c = 102.057 | γ = 90 |
Symmetry | |
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Space Group | P 41 3 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 | 100 | CCD | ADSC QUANTUM 4 | 2002-04-25 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MARRESEARCH | 2003-04-11 | M | MAD | ||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | 1.199998 | CHESS | F1 |
2 | SYNCHROTRON | NSLS BEAMLINE X9A | 0.979383, 0.979228, 0.971708 | NSLS | X9A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.2 | 50 | 99.7 | 9700 | 9700 | 2 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 2.2 | 2.28 | 99.8 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.2 | 19.65 | 2 | 9700 | 9700 | 467 | 100 | 0.21031 | 0.21031 | 0.20842 | 0.2 | 0.24948 | 0.23 | RANDOM | 37.566 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 7.551 |
r_dihedral_angle_1_deg | 6.951 |
r_scbond_it | 4.66 |
r_mcangle_it | 3.012 |
r_angle_refined_deg | 2.33 |
r_mcbond_it | 1.666 |
r_angle_other_deg | 1.037 |
r_symmetry_vdw_other | 0.445 |
r_symmetry_vdw_refined | 0.284 |
r_nbd_refined | 0.269 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 797 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELXD | phasing |