1RKA
THE APO FORM OF E. COLI RIBOKINASE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1RKD | 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.8 | CRYSTALS WERE GROWN IN 22-33% PEG 2000, MONO-METHYLETHER AS PRECIPITANT AND BUFFERED TO PH 4.8 WITH 0.1 M NA ACETATE. CRYO-PROTECTANT: MOTHER LIQUID ALSO CONTAINING 15% ETHYLENEGLYCOL. SOAK-TIME: 2-3 MINUTES. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 40.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 61.97 | ¦Á = 90 |
b = 61.97 | ¦Â = 90 |
c = 127.834 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 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 | MIRRORS | 1998-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | MAX II | I711 |
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 | 2.3 | 15 | 96.4 | 0.056 | 20.6 | 5.5 | 12644 | 32 |
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 | 2.3 | 2.34 | 87.5 | 0.235 | 6.7 | 5.5 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309. | 2.3 | 15 | 12644 | 12644 | 619 | 96.3 | 0.21 | 0.253 | RANDOM | 27 |
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] | |
-2.84 | -1.66 | -2.84 | 5.685 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 23.1 |
x_scangle_it | 2.5 |
x_scbond_it | 1.8 |
x_mcangle_it | 1.7 |
x_angle_deg | 1.5 |
x_mcbond_it | 1.1 |
x_improper_angle_d | 0.76 |
x_bond_d | 0.007 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2236 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |