2FAW
crystal structure of papaya glutaminyl cyclase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 85 mM Tris-HCl, 0.17 M sodium acetate, 25% PEG 4000, 15% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.82 | α = 90 |
b = 81.2 | β = 90 |
c = 108.17 | 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 | MARMOSAIC 225 mm CCD | toroidal focussing mirror | 2004-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.953718, 1.77122 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.7 | 19.537 | 99.9 | 0.06 | 41.6 | 28.9 | 61500 | 61500 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.8 | 100 | 0.279 | 15.3 | 29.3 | 9594 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.7 | 19.537 | 61499 | 3075 | 100 | 0.167 | 0.165 | 0.208 | RANDOM | 23.37 |
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] | |
-0.07 | 0.89 | -0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.815 |
r_scangle_it | 3.027 |
r_scbond_it | 2.015 |
r_angle_refined_deg | 1.933 |
r_sphericity_free | 1.897 |
r_sphericity_bonded | 1.797 |
r_mcangle_it | 1.484 |
r_rigid_bond_restr | 0.986 |
r_mcbond_it | 0.889 |
r_nbd_refined | 0.243 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4124 |
Nucleic Acid Atoms | |
Solvent Atoms | 897 |
Heterogen Atoms | 101 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SCALE | data reduction |
XDS | data scaling |
SHARP | phasing |