3CSM
STRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOXABICYCLIC INHIBITOR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CSM | PDB ENTRY 1CSM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | HANGING DROP, 19 % (W/V) PEG MONOMETHYLETHER 5000, 5 MM DTT, 0.15 M TRIS PH 8.0, 0.15 M SODIUM ACETATE, 16 MM TRYPTOPHAN, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.3 | 71.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 203.5 | α = 90 |
b = 203.5 | β = 90 |
c = 128.7 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | 123 | AREA DETECTOR | SIEMENS-NICOLET X100 | SUPPER DOUBLE-MIRRORS | 1996-10-15 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ELLIOTT GX-13 |
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 | 3 | 20 | 98.4 | 0.092 | 2.5 | 20253 |
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 | 3 | 3.2 | 99.1 | 0.325 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB ENTRY 1CSM | 3 | 15 | 2 | 16930 | 0.204 | 0.204 | 0.247 | RANDOM | 38.6 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 19 |
x_scangle_it | 7.523 |
x_scbond_it | 5.144 |
x_mcangle_it | 4.856 |
x_mcbond_it | 3.087 |
x_angle_deg | 2 |
x_improper_angle_d | 1.7 |
x_bond_d | 0.013 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4144 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XDS | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |