1JCS
CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH THE PEPTIDE SUBSTRATE TKCVFM AND AN ANALOG OF FARNESYL DIPHOSPHATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1D8D | PDB ENTRY 1D8D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.7 | 290 | PEG 8000, Ammonium Acetate, DTT, Tris-HCl, pH 5.7, VAPOR DIFFUSION, HANGING DROP at 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.13 | 60.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 170.921 | α = 90 |
b = 170.921 | β = 90 |
c = 69.425 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | Mirrors | 1999-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 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 | 2.2 | 50 | 93.8 | 0.067 | 17.2 | 5.1 | 58693 | 55202 | 31.8 |
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 | 2.2 | 2.23 | 100 | 0.269 | 2.64 | 4.98 | 1953 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1D8D | 2.2 | 50 | 2 | 58693 | 52877 | 2633 | 89.7 | 0.162 | 0.16 | 0.16 | 0.202 | FROM PDB ENTRY 1D8D | 34.5 |
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] | |
-1.652 | 0.294 | -1.652 | 8.143 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 21.2 |
x_scangle_it | 5.63 |
x_scbond_it | 3.78 |
x_mcangle_it | 3.18 |
x_mcbond_it | 2.03 |
x_improper_angle_d | 1.32 |
x_angle_deg | 1.3 |
x_bond_d | 0.008 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5997 |
Nucleic Acid Atoms | |
Solvent Atoms | 436 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |