4HX0
Crystal structure of a putative nucleotidyltransferase (TM1012) from Thermotoga maritima at 1.87 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FCL |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5.5 | 293 | Crystallization by hanging drop with MPD as a precipitant, pH 5.5, EVAPORATION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.196 | α = 90 |
b = 52.722 | β = 105.05 |
c = 53.508 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2011-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | KURCHATOV SNC BEAMLINE K4.4 | 0.972 | KURCHATOV SNC | K4.4 |
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 | 1.87 | 11.86 | 97 | 0.029 | 3.18 | 14084 | 13662 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.87 | 1.94 | 95.4 | 0.105 | 0.129 | 8.7 | 2.72 | 1387 |
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 | 2FCL | 1.87 | 12 | 14084 | 12979 | 682 | 96.56 | 0.1758 | 0.1758 | 0.17237 | 0.24459 | RANDOM | 27.638 |
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] | |
0.35 | -0.94 | -0.34 | -0.5 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.248 |
r_dihedral_angle_4_deg | 19.964 |
r_dihedral_angle_3_deg | 15.77 |
r_dihedral_angle_1_deg | 5.376 |
r_angle_refined_deg | 1.457 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1350 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 115 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
AMoRE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |