4WU3
Structure of the PTP-like myo-inositol phosphatase from Mitsuokella multacida in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3F41 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | PEG 8000, Polyethylene glycol, Tris chloride, beta-mercapto ethanol, glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.899 | α = 107.27 |
b = 86.68 | β = 91.69 |
c = 124.149 | γ = 90.01 |
Symmetry | |
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Space Group | P 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 | RAYONIX MX-300 | 2011-02-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | .97934 | CLSI | 08ID-1 |
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 | 2.2 | 44.54 | 98.8 | 0.08 | 6 | 2.2 | 146418 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 2.24 | 96.6 | 0.16 | 4.3 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3F41 | 2.2 | 44.54 | 144299 | 2118 | 98.07 | 0.19014 | 0.18979 | 0.21341 | RANDOM | 19.523 |
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] | |
-0.13 | -0.13 | -0.13 | -2.05 | -0.66 | 2.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.849 |
r_dihedral_angle_4_deg | 13.831 |
r_dihedral_angle_3_deg | 12.264 |
r_dihedral_angle_1_deg | 5.515 |
r_mcangle_it | 2.804 |
r_mcbond_it | 1.822 |
r_mcbond_other | 1.82 |
r_angle_refined_deg | 1.106 |
r_angle_other_deg | 0.67 |
r_chiral_restr | 0.057 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19188 |
Nucleic Acid Atoms | |
Solvent Atoms | 2262 |
Heterogen Atoms | 270 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOLREP | phasing |
Aimless | data scaling |
MOSFLM | data reduction |