3ZL6
Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZCD | PDB ENTRY 3ZCD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 0.2 M MGCL2, 20% PEG6000, 0.1 M TRISCL PH 8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.16 | α = 90 |
b = 98.84 | β = 90 |
c = 131.55 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | 2011-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 1.85 | 32.26 | 99.6 | 0.12 | 8.2 | 4.5 | 47364 | 2 |
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) | |||||||||||
1 | 1.85 | 1.95 | 100 | 0.72 | 1.9 | 4.4 |
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 | SIR | THROUGHOUT | PDB ENTRY 3ZCD | 1.85 | 31.35 | 44882 | 2339 | 99.03 | 0.17774 | 0.17545 | 0.22222 | RANDOM | 22.21 |
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] | |
0.57 | -0.85 | 0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.405 |
r_dihedral_angle_4_deg | 20.173 |
r_dihedral_angle_3_deg | 14.085 |
r_dihedral_angle_1_deg | 5.146 |
r_angle_refined_deg | 1.775 |
r_angle_other_deg | 1.276 |
r_symmetry_vdw_refined | 0.342 |
r_nbd_refined | 0.267 |
r_symmetry_vdw_other | 0.237 |
r_nbd_other | 0.222 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4086 |
Nucleic Acid Atoms | |
Solvent Atoms | 429 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |