1I6T
STRUCTURE OF INORGANIC PYROPHOSPHATASE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IGP | PDB ENTRY 1IGP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | NULL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.356 | α = 90 |
b = 109.356 | β = 90 |
c = 75.582 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | IMAGE PLATE | MAR scanner 345 mm plate | MIRRORS | 1998-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.906 | EMBL/DESY, HAMBURG | X11 |
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 | 1.2 | 20 | 96.1 | 0.036 | 0.026 | 17.1 | 12.3 | 640235 | 640235 | 17.6 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.2 | 1.21 | 90.1 | 0.441 | 53.5 | 3.6 | 4.8 | 1618 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1IGP | 1.2 | 12 | 49270 | 49270 | 2599 | 91.3 | 0.129 | 0.129 | 0.129 | 0.17 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
2 | 1247 | 1577 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_zero_chiral_vol | 0.09 |
s_non_zero_chiral_vol | 0.09 |
s_approx_iso_adps | 0.09 |
s_similar_adp_cmpnt | 0.06 |
s_angle_d | 0.03 |
s_anti_bump_dis_restr | 0.02 |
s_bond_d | 0.01 |
s_similar_dist | |
s_from_restr_planes | |
s_rigid_bond_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1380 |
Nucleic Acid Atoms | |
Solvent Atoms | 254 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |