3JSY
N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 295 | KSCN, PEG4000, NaAcetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57 | α = 90 |
b = 70.08 | β = 90 |
c = 97.96 | 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 | Multilayer mirror | 2009-04-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-5 | 0.90778 | MAX II | I911-5 |
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 | 1.6 | 20 | 92.5 | 0.056 | 21.61 | 4.7 | 50801 |
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 | 1.6 | 1.7 | 85 | 0.38 | 4.45 | 4.7 | 7327 |
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 | Solved with MAD and refined against native data set | THROUGHOUT | 1.6 | 15 | 52013 | 49365 | 2648 | 99.2 | 0.229 | 0.18412 | 0.1816 | 0.23321 | RANDOM | 29.389 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.56 | 1.83 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.983 |
r_sphericity_free | 18.563 |
r_sphericity_bonded | 15.384 |
r_dihedral_angle_4_deg | 12.533 |
r_dihedral_angle_3_deg | 10.868 |
r_scangle_it | 7.659 |
r_scbond_it | 5.002 |
r_mcangle_it | 4.709 |
r_dihedral_angle_1_deg | 3.576 |
r_rigid_bond_restr | 3.519 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3207 |
Nucleic Acid Atoms | |
Solvent Atoms | 392 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHENIX | model building |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |