1GQT
Activation of Ribokinase by Monovalent Cations
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.8 | CRYSTALS WERE GROWN IN DROPS CONTAINING 0.3 MM WILD-TYPE RK, 5 MM D-RIBOSE, 10 MM AMP-PCP, 75 MM MGCL2, 60 MM CSCL, 10% 2-METHYL-2,4-PENTANEDIOL, 10% POLYETHYLENE GLYCOL 4000 AND 50 MM SODIUM ACETATE, PH 4.8. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 55.453 | ¦Á = 90 |
b = 62.767 | ¦Â = 90 |
c = 339.277 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | MARRESEARCH | 2000-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 2.34 | 17 | 98.2 | 0.091 | 10.9 | 4.9 | 50296 |
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 | 2.34 | 2.38 | 99.9 | 0.377 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | OTHER | THROUGHOUT | 2.34 | 17 | 50296 | 2480 | 98.2 | 0.196 | 0.193 | 0.257 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 8.007 |
r_scbond_it | 5.394 |
r_mcangle_it | 3.154 |
r_mcbond_it | 1.924 |
r_angle_other_deg | 1.574 |
r_nbd_refined | 0.268 |
r_symmetry_vdw_refined | 0.254 |
r_symmetry_hbond_refined | 0.16 |
r_xyhbond_nbd_refined | 0.157 |
r_metal_ion_refined | 0.148 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8976 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 137 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |