7MDC
Full-length wildtype ClbP inhibited by hexanoyl-D-asparagine boronic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7MDE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 295 | Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 11 mM (S)-N-(3-amino-3-oxo-1-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)propyl)hexanamide plus 3.5 parts 0.1M tris pH 7.2, 25%(v/v) PEG400, 200 mM Li2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.88 | 68.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.718 | α = 90 |
b = 96.718 | β = 90 |
c = 183.382 | γ = 90 |
Symmetry | |
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Space Group | P 42 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 | PIXEL | DECTRIS EIGER X 16M | 2019-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.98 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.7 | 45.58 | 99.88 | 0.2575 | 0.2702 | 0.08088 | 0.996 | 8.06 | 10.9 | 24663 | 48.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.7 | 2.797 | 99.92 | 1.887 | 1.975 | 0.5802 | 0.534 | 11.5 |
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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7MDE | 2.7 | 45.58 | 24644 | 1231 | 99.88 | 0.1926 | 0.2359 | 57.88 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.0649 |
f_angle_d | 0.9222 |
f_chiral_restr | 0.0518 |
f_plane_restr | 0.0082 |
f_bond_d | 0.0071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3315 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHENIX | phasing |