1O5K
Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DHP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 7.5 | 293 | 28% PEG-400, 0.1M Sodium HEPES pH 7.5, 0.2M Calcium chloride dihydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.672 | α = 90 |
b = 140.768 | β = 90 |
c = 155.943 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 4 | bent conical Si-mirror (Rh coating) | 2003-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.61 | 50 | 100 | 0.096 | 12.18 | 4.25 | 68682 | 68682 | 30.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.61 | 1.67 | 65.47 | 0.712 | 1.04 | 1.74 | 5042 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1DHP | 1.8 | 35.61 | 49783 | 2656 | 93.33 | 0.14174 | 0.13941 | 0.18593 | RANDOM | 25.358 |
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] | |
1.84 | -0.51 | -1.32 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.241 |
r_dihedral_angle_4_deg | 20.002 |
r_dihedral_angle_3_deg | 13.619 |
r_scangle_it | 7.692 |
r_dihedral_angle_1_deg | 6.139 |
r_scbond_it | 5.534 |
r_mcangle_it | 3.014 |
r_mcbond_it | 2.275 |
r_angle_refined_deg | 1.608 |
r_angle_other_deg | 0.857 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4539 |
Nucleic Acid Atoms | |
Solvent Atoms | 508 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |