4CM7
Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2C7V | PDB ENTRY 2C7V |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.607 | α = 90 |
b = 89.999 | β = 115.51 |
c = 82.381 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RIGAKU SATURN 944 HG | 2012-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF |
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 | 1.9 | 40.82 | 92.8 | 0.08 | 17.3 | 3.8 | 71727 |
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 | 1.9 | 2 | 76.1 | 0.37 | 5.1 | 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 | PDB ENTRY 2C7V | 1.9 | 40.82 | 68055 | 3645 | 92.53 | 0.13708 | 0.13485 | 0.17864 | RANDOM | 15.751 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.08 | -0.48 | 2.21 | -0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.264 |
r_dihedral_angle_4_deg | 19.831 |
r_dihedral_angle_3_deg | 13.39 |
r_dihedral_angle_1_deg | 6.056 |
r_mcangle_it | 2.266 |
r_scbond_it | 1.715 |
r_angle_refined_deg | 1.632 |
r_mcbond_it | 1.355 |
r_mcbond_other | 1.354 |
r_angle_other_deg | 0.823 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7490 |
Nucleic Acid Atoms | |
Solvent Atoms | 774 |
Heterogen Atoms | 284 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |