4L95
Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 291 | 10%(w/v) PEG 8000, 0.2M NaCl, 0.1M Na/K buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 226.505 | α = 90 |
b = 61.341 | β = 101.37 |
c = 156.956 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 110 | CCD | Bruker DIP-6040 | 2012-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 1.0 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.34 | 30 | 98 | 88182 | 88182 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.34 | 2.42 | 98 |
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 | 1L9X | 2.34 | 29.76 | 83768 | 83768 | 4413 | 98.21 | 0.25 | 0.24273 | 0.2395 | 0.30407 | RANDOM | 50.285 |
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] | |
0.01 | -0.04 | 0.03 | -0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.001 |
r_dihedral_angle_4_deg | 22.568 |
r_dihedral_angle_3_deg | 19.557 |
r_dihedral_angle_1_deg | 7.384 |
r_scangle_it | 3.554 |
r_scbond_it | 2.23 |
r_angle_refined_deg | 1.671 |
r_mcangle_it | 1.577 |
r_mcbond_it | 0.861 |
r_chiral_restr | 0.12 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13842 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
X-PLOR | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
X-PLOR | phasing |