1TKK
The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JPM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored at -80 C. The frozen concentrated protein was thawed and diluted to 10 mg/mL with 5 mM HEPES, 2 mM MgCl2, 1 mM NaN3, pH 7.5. A stock solution of the peptide substrate L-Ala-L-Glu (Sigma) was neutralized to pH 7.5 with NaOH and brought to a final concentration of 1.6 M. This solution was added to the protein as 1/50th part by volume and the resultant mixture utilized for crystallization experiments. The initial crystals were grown by hanging drop by mixing 5 ?l of protein solution and 5 ?l of a solution containing 9-11% dimethyl-PEG 5000, 50 mM MOPS, 1% MPD, 1 mM NaN3, pH 7.0 and suspending the droplets over 600 ?l precipitant at 20 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.4 | α = 90 |
b = 134.6 | β = 90 |
c = 194.9 | γ = 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 | 150 | CCD | CUSTOM-MADE | 2001-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0 | APS | 19-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 | 50 | 96.7 | 0.159 | 8.6 | 6.2 | 173946 | 173946 |
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) | |||||||||||
2.1 | 2.18 | 96.7 | 0.508 | 2.6 | 6.4 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1JPM | 2.1 | 30 | 173500 | 164780 | 8685 | 96.51 | 0.222 | 0.222 | 0.219 | 0.285 | RANDOM | 25.435 |
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] | |
-1.64 | 1.87 | -0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.733 |
r_scangle_it | 3.933 |
r_mcangle_it | 2.815 |
r_scbond_it | 2.637 |
r_mcbond_it | 1.967 |
r_angle_refined_deg | 1.199 |
r_angle_other_deg | 0.78 |
r_nbd_other | 0.22 |
r_symmetry_hbond_refined | 0.194 |
r_nbd_refined | 0.192 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21626 |
Nucleic Acid Atoms | |
Solvent Atoms | 1521 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
MOLREP | phasing |