2AJR
Crystal structure of Possible 1-phosphofructokinase (EC 2.7.1.56) (tm0828) from Thermotoga Maritima at 2.46 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 293 | 16% PEG-8000, 0.08M sodium cacodylate, 0.16M magnesium acetate tetrahydrate, 20% glyerol anhyrous , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 57.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.796 | α = 90 |
b = 115.796 | β = 90 |
c = 124.828 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | FLAT MIRROR | 2002-06-17 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.885567,0.976224 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 29.2 | 99.5 | 0.109 | 0.109 | 5.9 | 6.3 | 31322 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.46 | 2.52 | 95 | 0.633 | 0.633 | 1.2 | 3.5 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.46 | 28.49 | 29692 | 1595 | 99.4 | 0.193 | 0.24 | RANDOM | 31.77 |
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] | |
1.31 | 1.31 | -2.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.829 |
r_dihedral_angle_3_deg | 17.005 |
r_dihedral_angle_4_deg | 15.688 |
r_scangle_it | 6.864 |
r_dihedral_angle_1_deg | 6.194 |
r_scbond_it | 5.131 |
r_mcangle_it | 2.525 |
r_mcbond_it | 1.719 |
r_angle_refined_deg | 1.274 |
r_angle_other_deg | 0.825 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5013 |
Nucleic Acid Atoms | |
Solvent Atoms | 42 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
SnB | phasing |
MLPHARE | phasing |
SOLVE | phasing |