5F5B
Structure of E.Coli GlpG complexed with peptidic inhibitor Ac-VRMA-CHO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IC8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 4M NaNO3, 0.1M Tris pH7.5, 5% Glycerol, 0.2 % nonyl glucoside |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.59 | α = 90 |
b = 110.59 | β = 90 |
c = 126.73 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 270 | 2014-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | 0.972 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 50.01 | 99.3 | 8.2 | 7.9 | 20167 |
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 | 2IC8 | 2.3 | 50.01 | 20167 | 651 | 98.7 | 0.215 | 0.213 | 0.249 | RANDOM | 55.12 |
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] | |
-1.26 | -0.63 | -1.26 | 4.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.889 |
r_dihedral_angle_4_deg | 23.752 |
r_dihedral_angle_3_deg | 17.329 |
r_long_range_B_refined | 13.41 |
r_dihedral_angle_1_deg | 10.06 |
r_mcangle_it | 8.211 |
r_scbond_it | 7.291 |
r_mcbond_it | 5.727 |
r_angle_refined_deg | 2.478 |
r_chiral_restr | 0.14 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1485 |
Nucleic Acid Atoms | |
Solvent Atoms | 34 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |