4TMR
Crystal structure of ternary complex of Plasmodium vivax SHMT with glycine and a novel pyrazolopyran 99S: methyl 5-{3-[(4S)-6-amino-5-cyano-3-methyl-4-(propan-2-yl)-2,4-dihydropyrano[2,3-c]pyrazol-4-yl]-5-cyanophenyl}thiophene-2-carboxylate .
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 297 | PEG4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.813 | α = 90 |
b = 58.26 | β = 90.01 |
c = 234.96 | 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 | CCD | ADSC QUANTUM 315r | Rh Coated mirrors | 2013-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1.0 | NSRRC | BL13B1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.7 | 30 | 92.2 | 0.016 | 62.9 | 3.9 | 34845 | 49.6 |
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 | 2.7 | 2.8 | 81.4 | 0.042 | 4.1 |
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 | THROUGHOUT | PDB ENTRY 4OYT | 2.7 | 30 | 34823 | 3461 | 91.9 | 0.217 | 0.21 | 0.278 | RANDOM | 32.42 |
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] | |
0.03 | 0.84 | 0.4 | -0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.538 |
r_dihedral_angle_3_deg | 19.096 |
r_dihedral_angle_4_deg | 18.453 |
r_dihedral_angle_1_deg | 5.759 |
r_angle_refined_deg | 1.427 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10374 |
Nucleic Acid Atoms | |
Solvent Atoms | 217 |
Heterogen Atoms | 161 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |