2BF7
Leishmania major pteridine reductase 1 in complex with NADP and biopterin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E92 | PDB ENTRY 1E92 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 293 | 15 MG/ML PROTEIN, 0.1M NAAC/HAC BUFFER PH 5.5, 9% MPEG 5000, 0.05M CAAC2, 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 95.269 | ¦Á = 90 |
b = 104.554 | ¦Â = 90 |
c = 138.069 | ¦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 | CCD | ADSC CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX9.6 | SRS | PX9.6 |
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 | 2.4 | 25 | 86.9 | 0.1 | 12.9 | 4.3 | 47504 | 37.8 |
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 | 2.4 | 2.5 | 76.5 | 0.29 | 3.7 |
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 1E92 | 2.4 | 24.77 | 45056 | 2385 | 100 | 0.22 | 0.219 | 0.242 | RANDOM | 33.27 |
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] | |
-0.07 | -0.14 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 2.894 |
r_scangle_it | 2.543 |
r_scbond_it | 1.497 |
r_angle_refined_deg | 1.359 |
r_mcangle_it | 1.087 |
r_mcbond_it | 0.559 |
r_symmetry_hbond_refined | 0.307 |
r_nbd_refined | 0.195 |
r_symmetry_vdw_refined | 0.185 |
r_xyhbond_nbd_refined | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7711 |
Nucleic Acid Atoms | |
Solvent Atoms | 268 |
Heterogen Atoms | 280 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |