4CNF
Crystal structure of Sulfolobus acidocaldarius TrmJ
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CND | PDB ENTRY 4CND |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 0.2 M KBR, 0.1M NA-ACETATE PH 5.5, 20 % PEG2000MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.138 | α = 90 |
b = 53.702 | β = 90 |
c = 130.308 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | 100 | PIXEL | DECTRIS PILATUS | 2013-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 1.4 | 43 | 99.9 | 0.01 | 11.1 | 14.4 | 63289 | 1.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.4 | 1.5 | 99.3 | 1.2 | 14 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4CND | 1.4 | 42.69 | 60181 | 3069 | 99.72 | 0.1586 | 0.1568 | 0.19276 | RANDOM | 21.534 |
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] | |
0.2 | -0.34 | 0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.671 |
r_sphericity_free | 17.393 |
r_dihedral_angle_3_deg | 13.496 |
r_rigid_bond_restr | 12.622 |
r_dihedral_angle_4_deg | 12.57 |
r_sphericity_bonded | 10.044 |
r_dihedral_angle_1_deg | 6.202 |
r_scbond_it | 5.305 |
r_angle_other_deg | 3.751 |
r_mcangle_it | 3.563 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2455 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |