6QXH
Crystal structure of His-tag human thymidylate synthase (HT-hTS) in complex with dUMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HWY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 293 | 27-30 % wt/vol PEG4000, 30 mM ammonium sulfate and 0.1 M TRIS, pH 9 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.43 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 182.11 | ¦Á = 90 |
b = 61.59 | ¦Â = 115.38 |
c = 101.1 | ¦Ã = 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 | PIXEL | DECTRIS PILATUS 6M | 2015-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.97625 | PETRA III, EMBL c/o DESY | P14 (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 | 2.04 | 34.19 | 97 | 0.066 | 0.072 | 0.028 | 0.998 | 12.8 | 6.3 | 62630 | 2 | 43.18 |
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 | 2.04 | 2.15 | 97.2 | 0.484 | 0.528 | 0.206 | 0.937 | 3.3 | 6.4 |
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 | 1HWY | 2.04 | 34.19 | 58183 | 4434 | 96.69 | 0.19031 | 0.18665 | 0.23676 | RANDOM | 69.393 |
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] | |
1.17 | 2.87 | -2.98 | -0.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.943 |
r_dihedral_angle_4_deg | 20.981 |
r_dihedral_angle_3_deg | 17.645 |
r_long_range_B_refined | 8.167 |
r_dihedral_angle_1_deg | 7.894 |
r_mcangle_it | 3.669 |
r_scbond_it | 3.253 |
r_mcbond_it | 2.639 |
r_angle_refined_deg | 1.94 |
r_chiral_restr | 0.137 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6804 |
Nucleic Acid Atoms | |
Solvent Atoms | 205 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |