2FVV
Human Diphosphoinositol polyphosphate phosphohydrolase 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | 30% PEG8000, 0.2M Lithium sulphate, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.653 | α = 90 |
b = 59.9 | β = 90 |
c = 61.735 | 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 | Bruker Platinum 135 | Helios Multilayer | 2005-12-27 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MARRESEARCH | Double crystal monochromator | 2005-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 | ||
2 | SYNCHROTRON | MAX II BEAMLINE I911-5 | 0.97957 | MAX II | I911-5 |
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 | 1.25 | 27.44 | 90.5 | 0.0809 | 23.93 | 8.88 | 50655 | 45852 | -3 |
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) | |||||||||||
1.25 | 1.34 | 58.1 | 0.2757 | 2.74 | 1.55 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R | 1.25 | 10 | 50655 | 45852 | 922 | 90.5 | 0.173 | 0.171 | 0.171 | 0.222 | RANDOM | 25.492 |
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 |
s_approx_iso_adps | 0.122 |
s_non_zero_chiral_vol | 0.109 |
s_similar_adp_cmpnt | 0.071 |
s_zero_chiral_vol | 0.068 |
s_angle_d | 0.037 |
s_from_restr_planes | 0.031 |
s_bond_d | 0.017 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist | |
s_anti_bump_dis_restr |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1181 |
Nucleic Acid Atoms | |
Solvent Atoms | 192 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
SHELX | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data reduction |
SAINT | data reduction |
XDS | data reduction |
SADABS | data scaling |
XSCALE | data scaling |
SHELXD | phasing |
SHELXL-97 | refinement |