3DYG
T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2EWG | PDB ENTRY 2EWG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.75 | 298 | 10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.39 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 135.565 | ¦Á = 90 |
b = 118.52 | ¦Â = 112.36 |
c = 63.186 | ¦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 | 123.2 | CCD | ADSC QUANTUM 4 | 2006-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X8C | NSLS | X8C |
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 | 2.1 | 30 | 99.1 | 0.098 | 0.101 | 7.6 | 53536 | 17.3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.1 | 2.18 | 98.3 | 0.53 | 7.6 |
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 2EWG | 2.1 | 29.22 | 51405 | 1533 | 95.6 | 0.207 | 0.207 | 0.25 | RANDOM | 28.3 |
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] | |
4.05 | 2.89 | -5.78 | 1.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 18.9 |
c_scangle_it | 3.51 |
c_scbond_it | 2.63 |
c_mcangle_it | 2.35 |
c_mcbond_it | 1.7 |
c_angle_deg | 1.24 |
c_improper_angle_d | 0.83 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5742 |
Nucleic Acid Atoms | |
Solvent Atoms | 577 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |