6RXC
Leishmania major pteridine reductase 1 (LmPTR1) in complex with inhibitor 4 (NMT-C0026)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5L4N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.3 | 293 | Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH 5.3 and 10 mM DTT; Crystallization buffer: 12% PEG4600, 100 mM Sodium Acetate pH 5.5 and 120-160 mM Calcium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.12 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 95.267 | ¦Á = 90 |
b = 103.445 | ¦Â = 90 |
c = 136.749 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS3 6M | 2015-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.00000 | Diamond | I03 |
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 | 2.1 | 82.5 | 98.7 | 0.11 | 0.124 | 0.057 | 0.99 | 8.2 | 4.5 | 78229 | 2 | 24.1 |
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 | 2.1 | 2.21 | 99.4 | 0.383 | 0.434 | 0.2 | 0.836 | 3.6 | 4.5 |
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 | 5L4N | 2.1 | 82.5 | 74289 | 3890 | 98.39 | 0.21586 | 0.21345 | 0.26082 | RANDOM | 28.602 |
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] | |
-0.01 | 0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.643 |
r_dihedral_angle_4_deg | 18.845 |
r_dihedral_angle_3_deg | 16.062 |
r_dihedral_angle_1_deg | 7.649 |
r_long_range_B_refined | 7.023 |
r_mcangle_it | 4.181 |
r_scbond_it | 3.677 |
r_mcbond_it | 3.047 |
r_angle_refined_deg | 1.923 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7687 |
Nucleic Acid Atoms | |
Solvent Atoms | 651 |
Heterogen Atoms | 336 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |