5YG4
Plasmodium vivax SHMT bound with PLP-glycine and S-GS849
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4TMR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 8.5 | 298 | PEG 4000, 0.06-0.12M NaCl, 0.1M Tris-HCl pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.848 | α = 90 |
b = 58.207 | β = 89.99 |
c = 234.497 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | CMOS | BRUKER PHOTON 100 | 2017-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER D8 QUEST | 1.54 |
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 | 2.3 | 30 | 99.5 | 0.071 | 0.077 | 0.029 | 0.998 | 17 | 6.3 | 60621 |
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 | 2.3 | 2.36 | 99.9 | 0.287 | 0.335 | 0.171 | 0.918 | 3.6 |
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 | 4TMR | 2.3 | 30 | 54697 | 5926 | 99.47 | 0.2211 | 0.2149 | 0.278 | RANDOM | 29.674 |
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] | |
0.6 | -0.2 | 1.86 | -2.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.183 |
r_dihedral_angle_3_deg | 18.379 |
r_dihedral_angle_4_deg | 14.229 |
r_dihedral_angle_1_deg | 5.684 |
r_angle_refined_deg | 1.567 |
r_angle_other_deg | 0.981 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10374 |
Nucleic Acid Atoms | |
Solvent Atoms | 370 |
Heterogen Atoms | 182 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |