2XAR
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP6.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XAM | PDB ENTRY 2XAM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.9 | 22% PEG 3350, 100 MM BIS-TRIS PH 5.9 2MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-6-P |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.67 | α = 90 |
b = 112.501 | β = 90 |
c = 139.72 | 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 | 120 | CCD | ADSC CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
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 | 2.6 | 112.5 | 100 | 0.12 | 5.76 | 7.63 | 17187 | 2 | 67.1 |
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 | 3.1 | 3.27 | 100 | 0.44 | 1.78 | 7.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 2XAM | 3.1 | 112.5 | 16316 | 870 | 99.95 | 0.24103 | 0.23803 | 0.29888 | RANDOM | 32 |
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] | |
-1.45 | 0.92 | 0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.597 |
r_dihedral_angle_4_deg | 21.333 |
r_dihedral_angle_3_deg | 18.371 |
r_dihedral_angle_1_deg | 5.131 |
r_scangle_it | 1.556 |
r_angle_refined_deg | 1.19 |
r_scbond_it | 0.841 |
r_mcangle_it | 0.809 |
r_mcbond_it | 0.429 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6677 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
MOLREP | phasing |