3MX1
The structure of GIY-YIG endonuclease R.Eco29kI
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 0.1M Tris HCl, 1.5M NaCl, 10% ethanol v/v, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.28 | 62.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.906 | α = 90 |
b = 90.074 | β = 90 |
c = 88.85 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 110 | CCD | ADSC QUANTUM 315 | 2009-07-29 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 315 | 2009-10-28 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 1.0 | ALS | 5.0.1 |
2 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.9801, 0.9802, 0.975 | ALS | 5.0.2 |
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 | ||||||||
1,2 | 2.3 | 62.91 | 98.82 | 0.079 | 18.35 | 4.9 | 15893 | 15078 |
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) | |||||||||||
2.3 | 2.358 | 94.2 | 0.311 | 4.2 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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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 | MAD | THROUGHOUT | Phase information by PHENIX | 2.3 | 50 | 15893 | 15078 | 791 | 98.82 | 0.18507 | 0.18285 | 0.22781 | RANDOM | 42.06 |
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] | |
0.62 | 1.97 | -2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.557 |
r_dihedral_angle_3_deg | 15.522 |
r_dihedral_angle_4_deg | 14.827 |
r_dihedral_angle_1_deg | 7.659 |
r_scangle_it | 5.291 |
r_scbond_it | 3.38 |
r_mcangle_it | 2.346 |
r_angle_refined_deg | 1.951 |
r_mcbond_it | 1.279 |
r_chiral_restr | 0.139 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1640 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |