1VHA
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
X-RAY DIFFRACTION
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.715 | α = 90 |
b = 104.715 | β = 90 |
c = 195.864 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 | CCD | MARRESEARCH | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 32-ID | 0.9795 | APS | 32-ID |
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 | 2.35 | 45.55 | 99.9 | 0.084 | 20.3 | 7.65 | 43711 | 43711 |
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 | 2.35 | 2.43 | 99.9 | 0.526 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.35 | 45.55 | 43711 | 2211 | 0.244 | 0.288 | 41.673 |
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] | |
0.282 | 0.282 | -0.565 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_scangle_it | 3.196 |
p_mcangle_it | 2.651 |
p_scbond_it | 2.164 |
p_mcbond_it | 1.551 |
p_angle_d | 1.404 |
p_planar_tor | 1.137 |
p_chiral_restr | 0.09 |
p_bond_d | 0.007 |
p_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6906 |
Nucleic Acid Atoms | |
Solvent Atoms | 226 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |