4UM4
STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH SULFATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MJW | PDB ENTRY 1MJW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.6 | 0.1M SODIUM ACETATE TRIHYDRATE, 2.0M AMMONIUM SULFATE,5 MM DTT, pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.44 | 72.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.044 | α = 90 |
b = 108.943 | β = 97.48 |
c = 81.014 | 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 | 100 | CCD | ADSC CCD | DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. | 2011-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.65 | 19.1 | 92 | 0.06 | 10.7 | 2.2 | 27508 | 45.79 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.65 | 2.65 | 94.1 | 0.43 | 2.4 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1MJW | 2.65 | 19.099 | 1.38 | 27498 | 1380 | 91.6 | 0.1954 | 0.1934 | 0.2346 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.328 |
f_angle_d | 1.394 |
f_chiral_restr | 0.086 |
f_bond_d | 0.011 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4143 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |