6W57
Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC069)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6W29 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 0.1 M HEPES, 1.2-1.4 M Na3-Citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.365 | α = 90 |
b = 73.365 | β = 90 |
c = 233.185 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 PILATUS 2M | 2019-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.4587 | LNLS | W01B-MX2 |
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 | 1.78 | 47.4 | 99.7 | 0.054 | 0.06 | 0.024 | 0.999 | 20.1 | 6 | 61897 |
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 | 1.78 | 1.82 | 99.9 | 0.86 | 0.949 | 0.391 | 0.645 | 5.5 |
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 | THROUGHOUT | 6W29 | 1.78 | 43.19 | 58740 | 3115 | 99.49 | 0.1792 | 0.178 | 0.2014 | RANDOM | 27.97 |
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] | |
0.29 | 0.29 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.985 |
r_dihedral_angle_4_deg | 13.948 |
r_dihedral_angle_3_deg | 13.936 |
r_dihedral_angle_1_deg | 6.273 |
r_angle_refined_deg | 1.723 |
r_angle_other_deg | 1.446 |
r_chiral_restr | 0.09 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4245 |
Nucleic Acid Atoms | |
Solvent Atoms | 332 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |