4LR9
Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3M8W | PDB ENTRY 3M8W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 17% PEG3350, 50 mM manganese chloride, 50 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 92.329 | ¦Á = 90 |
b = 76.615 | ¦Â = 108.96 |
c = 107.236 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | MARMOSAIC 300 mm CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.979 | APS | 21-ID-G |
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 | 2.1 | 50 | 99 | 0.087 | 17.5 | 81866 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.1 | 2.18 | 95.6 | 0.37 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3M8W | 2.1 | 20 | 78597 | 77794 | 4042 | 98.85 | 0.17126 | 0.1692 | 0.21267 | RANDOM | 29.648 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.08 | -0.37 | -1.19 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.584 |
r_dihedral_angle_4_deg | 16.121 |
r_dihedral_angle_3_deg | 14.199 |
r_dihedral_angle_1_deg | 5.626 |
r_angle_refined_deg | 1.2 |
r_mcangle_it | 0.755 |
r_scbond_it | 0.707 |
r_mcbond_it | 0.446 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9193 |
Nucleic Acid Atoms | |
Solvent Atoms | 691 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |