2OQ2
Crystal structure of yeast PAPS reductase with PAP, a product complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 30% w/v PEG 6000, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.418 | α = 90 |
b = 63.082 | β = 90 |
c = 323.96 | 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 | ADSC QUANTUM 4 | Si(1,1,1) | 2006-08-03 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2006-08-03 | M | MAD | ||||||
3 | 1 | |||||||||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97944 | SSRL | BL9-2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97879, 0.91838, 0.97931 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||
1,2 | 2.05 | 107.833 | 96.5 | 0.073 | 0.073 | 7.2 | 4.3 | 64994 | 62580 | 1 | 30.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
1,2 | 2.05 | 2.1 | 78.2 | 0.373 | 0.373 | 1.6 | 3 | 3655 |
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 | 2.1 | 40 | 55322 | 2802 | 98.23 | 0.196 | 0.193 | 0.246 | RANDOM | 36.637 |
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] | |
3.29 | -1.17 | -2.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.991 |
r_dihedral_angle_4_deg | 22.089 |
r_dihedral_angle_3_deg | 15.702 |
r_dihedral_angle_1_deg | 5.529 |
r_scangle_it | 1.606 |
r_angle_refined_deg | 1.178 |
r_scbond_it | 1.026 |
r_mcangle_it | 0.643 |
r_mcbond_it | 0.373 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8175 |
Nucleic Acid Atoms | |
Solvent Atoms | 333 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |