5UV4
Crystal Structure of Maize SIRK1 (sucrose-induced receptor kinase 1) kinase domain bound to AMP-PNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4L68 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0,02M of each monossacharide (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine), 0.1M MOPS/HEPES-Na pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.444 | α = 90 |
b = 74.532 | β = 90 |
c = 79.742 | 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 | PIXEL | DECTRIS PILATUS 6M-F | 2016-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.979200 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 2.3 | 39.87 | 97 | 0.049 | 0.027 | 0.998 | 14.8 | 4 | 14190 | 55.34 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.3 | 2.39 | 98.4 | 0.551 | 0.341 | 0.905 | 2.6 | 4.1 | 1492 |
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 | 4L68 | 2.3 | 39.87 | 14160 | 652 | 96.3 | 0.184 | 0.182 | 0.211 | RANDOM | 66.92 |
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] | |
24.0965 | -12.7082 | -11.3883 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.74 |
t_omega_torsion | 3.06 |
t_angle_deg | 1.06 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2180 |
Nucleic Acid Atoms | |
Solvent Atoms | 65 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |