1VI2
Crystal structure of shikimate-5-dehydrogenase with NAD
X-RAY DIFFRACTION
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.76 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 157.497 | ¦Á = 90 |
b = 157.497 | ¦Â = 90 |
c = 39.771 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 64 |
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 | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 32-ID | 1.5418, 0.9795 , 0.9641 | 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 | 2.1 | 38.18 | 98.7 | 0.059 | 16.4 | 3.79 | 32986 | 32986 |
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) | |||||||||||
2.1 | 2.18 | 91.4 | 0.176 | 3.6 |
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 | Se-Met MAD phasing | 2.1 | 38.18 | 32984 | 1674 | 0.234 | 0.3 | 30.282 |
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] | |
-0.606 | -0.303 | -0.606 | 0.909 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_scangle_it | 4.855 |
p_scbond_it | 3.472 |
p_mcangle_it | 3.215 |
p_planar_tor | 3.123 |
p_angle_d | 2.045 |
p_mcbond_it | 1.881 |
p_chiral_restr | 0.123 |
p_plane_restr | 0.016 |
p_bond_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4270 |
Nucleic Acid Atoms | |
Solvent Atoms | 275 |
Heterogen Atoms | 98 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |