3U6T
Crystal structure of the complex of type I Ribosome inactivating protein in complex with Kanamycin at 1.85 A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 298 | 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 130.02 | α = 90 |
b = 130.02 | β = 90 |
c = 39.83 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 77 | CCD | MARRESEARCH | mirror | 2011-10-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97 | ESRF | BM14 |
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 | 1.85 | 32.5 | 100 | 0.06 | 17 | 21429 | 21429 |
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) | |||||||||||
1 | 1.85 | 1.95 | 99.5 | 0.576 | 3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3MRW | 1.85 | 32.5 | 21429 | 20331 | 1098 | 99.99 | 0.19887 | 0.19796 | 0.19639 | 0.22774 | RANDOM | 32.44 |
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] | |
-1.55 | -0.78 | -1.55 | 2.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.987 |
r_dihedral_angle_3_deg | 12.857 |
r_dihedral_angle_4_deg | 12.851 |
r_dihedral_angle_1_deg | 4.897 |
r_scangle_it | 1.608 |
r_angle_refined_deg | 1.086 |
r_scbond_it | 0.891 |
r_mcangle_it | 0.67 |
r_mcbond_it | 0.353 |
r_chiral_restr | 0.078 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1911 |
Nucleic Acid Atoms | |
Solvent Atoms | 239 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |