1INI
CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1I52 | PDB ENTRY 1I52 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 279 | PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 129.99 | α = 90 |
b = 46.764 | β = 92.64 |
c = 38.387 | 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 | IMAGE PLATE | MARRESEARCH | flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) | 2001-01-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.773 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.8 | 90 | 98.6 | 0.026 | 0.026 | 26.4 | 2.8 | 20268 | 20268 | 1 | 1 | 21.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.81 | 1.83 | 98.6 | 0.308 | 2.7 | 2.9 | 641 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1I52 | 1.82 | 44 | 17144 | 17144 | 866 | 82.9 | 0.222 | 0.222 | 0.273 | RANDOM | 36.2 |
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] | |
-7.95 | -1.83 | 5 | 2.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.3 |
c_scangle_it | 5.84 |
c_scbond_it | 4.64 |
c_mcangle_it | 4.3 |
c_mcbond_it | 3.3 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.89 |
c_bond_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1716 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
CNS | phasing |