1VLU
Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | 0.175M Na Cl, 0.06M Acetic Acid, 20.00% MPD, 0.04M Acetate_Na, 0.01M Cymal , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K | |
2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 277 | .175M Na Cl, .06M Acetic Acid, 20% MPD, .04M Acetate_Na, 0.0008M Cymal-6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.58 | 65.6 |
4.36 | 71.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.041 | α = 90 |
b = 191.081 | β = 90 |
c = 125.57 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | ADSC QUANTUM 315 | flat mirror | 2002-07-02 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | Flat mirror | 2002-06-23 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | SSRL | BL11-1 | |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.97916, 0.97877, 0.90496 | SSRL | BL9-1 |
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 | ||||||||
1,2 | 2.29 | 47.83 | 91.7 | 0.1 | 13 | 4.5 | 60572 | 65.61 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.29 | 2.36 | 51.7 | 0.513 | 1.2 | 1.9 | 2500 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.29 | 47.83 | 57462 | 3075 | 91.23 | 0.2123 | 0.21043 | 0.24782 | RANDOM | 59.733 |
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] | |
-2.3 | 1.22 | 1.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 42.013 |
r_dihedral_angle_4_deg | 22.717 |
r_dihedral_angle_3_deg | 16.362 |
r_scangle_it | 7.886 |
r_dihedral_angle_1_deg | 5.898 |
r_scbond_it | 5.591 |
r_mcangle_it | 3.462 |
r_mcbond_it | 2.017 |
r_angle_refined_deg | 1.238 |
r_nbtor_refined | 0.294 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5912 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
RESOLVE | model building |
REFMAC | refinement |
CCP4 | data scaling |
RESOLVE | phasing |