4BEG
Structure of Rv2140c, a phosphatidyl-ethanolamine binding protein from Mycobacterium tuberculosis in complex with sulphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1M TRIS PH 8.0, 2.4 M AMMONIUM SULFATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.118 | α = 90 |
b = 62.118 | β = 90 |
c = 181.8 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | IMAGE PLATE | MAR scanner 345 mm plate | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
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 | 1.41 | 28.01 | 97.9 | 0.05 | 7.86 | 5.32 | 67729 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.41 | 1.49 | 87.2 | 0.27 | 2.81 | 5.23 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 4BEF | 1.42 | 27.248 | 67658 | 3427 | 99.189 | 0.151 | 0.1491 | 0.1949 | RANDOM | 15.055 |
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] | |
0.457 | 0.457 | -0.913 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.356 |
r_sphericity_free | 23.027 |
r_dihedral_angle_4_deg | 17.22 |
r_dihedral_angle_3_deg | 11.078 |
r_sphericity_bonded | 9.082 |
r_rigid_bond_restr | 7.082 |
r_dihedral_angle_1_deg | 6.562 |
r_angle_refined_deg | 2.017 |
r_chiral_restr | 0.148 |
r_bond_refined_d | 0.021 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2637 |
Nucleic Acid Atoms | |
Solvent Atoms | 345 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |