4H5E
Crystal structure of human FPPS in ternary complex with YS0470 and isopentenyl pyrophosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4DEM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 295 | 30% PEG 300, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.239 | α = 90 |
b = 111.239 | β = 90 |
c = 65.645 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2011-11-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 2.04 | 50 | 100 | 0.062 | 47.7 | 27.3 | 26486 | 26486 |
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 | 2.04 | 2.09 | 100 | 0.506 | 6.9 | 26.2 | 1289 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 4DEM | 2.04 | 50 | 24849 | 24849 | 1316 | 98.2 | 0.18805 | 0.18805 | 0.18573 | 0.23334 | RANDOM | 44.763 |
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] | |
-2.55 | -2.55 | 5.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.682 |
r_dihedral_angle_4_deg | 16.471 |
r_dihedral_angle_3_deg | 15.098 |
r_dihedral_angle_1_deg | 5.489 |
r_angle_refined_deg | 1.991 |
r_chiral_restr | 0.204 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2716 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |