5TQZ
Frutapin complexed with alpha-D-glucose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5KRP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 277 | 0.04 M Potassium monobasic phosphate, 20% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.023 | α = 90 |
b = 74.023 | β = 90 |
c = 185.522 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | PIXEL | DECTRIS PILATUS 6M-F | 2016-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96859 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.6 | 185.52 | 100 | 0.205 | 0.995 | 9.3 | 19.3 | 78721 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.63 | 100 | 0.2018 | 0.594 | 1.9 | 19.5 |
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 | FREE R-VALUE | 5krp | 1.6 | 64.11 | 74711 | 3914 | 99.98 | 0.15118 | 0.14907 | 0.1918 | RANDOM | 21.597 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.02 | -0.01 | -0.02 | 0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.07 |
r_dihedral_angle_3_deg | 16.215 |
r_dihedral_angle_4_deg | 16.01 |
r_dihedral_angle_1_deg | 9.001 |
r_long_range_B_refined | 5.039 |
r_long_range_B_other | 4.99 |
r_scangle_other | 3.16 |
r_angle_refined_deg | 2.903 |
r_mcangle_it | 2.598 |
r_mcangle_other | 2.598 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4608 |
Nucleic Acid Atoms | |
Solvent Atoms | 417 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data scaling |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |