2Q2X
Crystal Structure of the ECH2 decarboxylase domain of CurF from Lyngbya majuscula
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.15 | 277.15 | 1.5M sodium malonate pH 7.0, 50 mM HEPES pH 6.8, 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.433 | α = 90 |
b = 105.433 | β = 90 |
c = 46.314 | γ = 120 |
Symmetry | |
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Space Group | P 3 2 1 |
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 300 mm CCD | K-B pair of biomorph mirrors for vertical and horizontal focusing | 2006-08-16 | M | MAD | |||||
2 | 1 | |||||||||||||
3 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.0332,0.97942,0.97956,0.95373 | APS | 23-ID-B |
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 | 2 | 50 | 99.9 | 0.063 | 13.4 | 11 | 20390 | 20390 | 1 | 1 | 33.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2 | 2.07 | 100 | 0.682 | 3.6 | 10.4 | 2020 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 41.31 | 21970 | 20378 | 1024 | 99.91 | 0.204 | 0.202 | 0.25 | RANDOM | 37.711 |
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] | |
0.37 | 0.18 | 0.37 | -0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.897 |
r_dihedral_angle_3_deg | 15.587 |
r_dihedral_angle_4_deg | 12.505 |
r_scangle_it | 6.292 |
r_dihedral_angle_1_deg | 5.327 |
r_scbond_it | 4.054 |
r_mcangle_it | 1.782 |
r_angle_refined_deg | 1.245 |
r_mcbond_it | 1.037 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1887 |
Nucleic Acid Atoms | |
Solvent Atoms | 145 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
HKL-2000 | data reduction |