5D1F
Crystal structure of maize PDRP bound with AMP and Hg2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | peg, dioxane |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.04 | 75.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 175.514 | α = 90 |
b = 175.514 | β = 90 |
c = 175.514 | γ = 90 |
Symmetry | |
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Space Group | P 4 3 2 |
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 | 2013-06-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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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 | 3.4 | 50 | 100 | 0.092 | 0.092 | 55.5 | 217.2 | 13309 | 13309 | 3 | 3 |
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 | SAD | THROUGHOUT | 3.4 | 48.68 | 12469 | 661 | 98.73 | 0.22404 | 0.22305 | 0.24273 | RANDOM | 47.392 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.089 |
r_dihedral_angle_3_deg | 20.201 |
r_dihedral_angle_4_deg | 13.212 |
r_long_range_B_refined | 8.748 |
r_long_range_B_other | 8.748 |
r_dihedral_angle_1_deg | 7.051 |
r_mcangle_other | 5.175 |
r_mcangle_it | 5.174 |
r_scangle_other | 4.927 |
r_mcbond_it | 2.943 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1973 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
HKL-2000 | phasing |
HKL-2000 | data reduction |