3KYD
Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Y8Q | PDB ENTRY 1Y8Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 279 | 22% PEG 2000 MME, 0.2 M di-ammonium tartrate, 3% EtGly, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.717 | α = 90 |
b = 115.608 | β = 90 |
c = 90.837 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | ADSC QUANTUM 315 | 2008-10-27 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | CCD | ADSC QUANTUM 315 | 2008-11-09 | M | SINGLE WAVELENGTH | |||||||
1,2 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9790 | APS | 24-ID-C |
2 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9790 | APS | 24-ID-C |
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 | 2.6 | 25 | 99 | 0.074 | 15.8 | 33019 |
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) | |||||||||||
1,2 | 2.6 | 2.67 | 96.1 | 0.367 | 2.7 |
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 1Y8Q | 2.61 | 25 | 32957 | 1673 | 98.91 | 0.23 | 0.227 | 0.284 | RANDOM | 22.961 |
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] | |
0.47 | -2.72 | 2.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.978 |
r_dihedral_angle_4_deg | 15.983 |
r_dihedral_angle_3_deg | 15.472 |
r_dihedral_angle_1_deg | 4.23 |
r_angle_refined_deg | 0.897 |
r_scangle_it | 0.605 |
r_scbond_it | 0.352 |
r_mcangle_it | 0.337 |
r_mcbond_it | 0.181 |
r_chiral_restr | 0.056 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6724 |
Nucleic Acid Atoms | |
Solvent Atoms | 215 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |