3T80
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GHZ | PDB ENTRY 3GHZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | SATYA.00122.A.AN1 15 mg/mL, 222391E7 (10% PEG8000, 100 mM imidazole, pH 8.0, 200 mM calcium acetate, 2 mM zinc acetate, 2 mM magnesium chloride), cryosolvent (25% ethylene glycol, 2 mM zinc acetate, 2 mM magnsium chloride), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.91 | 68.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 200.013 | α = 90 |
b = 147.657 | β = 106.38 |
c = 56.919 | γ = 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 | 100 | CCD | RAYONIX MX-300 | 2011-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97949 | CLSI | 08ID-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 | 2.5 | 50 | 98.9 | 0.061 | 19.876 | 3.2 | 54267 |
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 | 2.5 | 2.54 | 99.8 | 0.501 | 3.2 |
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 3GHZ | 2.5 | 30 | 54128 | 2751 | 0.212 | 0.211 | 0.245 | RANDOM | 54.002 |
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] | |
2.35 | 3.57 | -1.25 | 0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.674 |
r_dihedral_angle_4_deg | 18.993 |
r_dihedral_angle_3_deg | 17.136 |
r_dihedral_angle_1_deg | 5.47 |
r_angle_other_deg | 2.976 |
r_angle_refined_deg | 1.744 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6693 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 190 |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |