3CK1
CRYSTAL STRUCTURE OF a putative thioesterase (REUT_A2179) FROM RALSTONIA EUTROPHA JMP134 AT 1.74 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | NANODROP, 4.3M NaCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.08 | 60.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.067 | α = 90 |
b = 77.067 | β = 90 |
c = 242.859 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-11-20 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97916, 0.97959, 0.91837 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.74 | 29.298 | 100 | 0.1 | 0.1 | 4.6 | 14.1 | 45201 | 22.19 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.74 | 1.79 | 100 | 0.812 | 0.812 | 0.9 | 6.1 | 3257 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.74 | 29.298 | 44869 | 2264 | 99.94 | 0.175 | 0.174 | 0.196 | RANDOM | 18.472 |
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] | |
0.52 | 0.26 | 0.52 | -0.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.25 |
r_dihedral_angle_4_deg | 20.815 |
r_dihedral_angle_3_deg | 12.006 |
r_scangle_it | 6.591 |
r_dihedral_angle_1_deg | 6.581 |
r_scbond_it | 4.797 |
r_mcangle_it | 3.126 |
r_mcbond_it | 1.973 |
r_angle_refined_deg | 1.676 |
r_angle_other_deg | 1.182 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2233 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXD | phasing |
autoSHARP | phasing |