4C1K
Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZCO | PDB ENTRY 1ZCO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | PROTEIN SOLUTION WAS MIXED 1:1 WITH CRYSTALIZATION SLUTION CONTAINING 100 MICROMCDCL2, 0.2M SODIUM CITRATE, 0.1M BTP, PH 6.5, 20% PEG3350. DROP SIZE WAS 2 MICRO L AND PROTEIN CONCENTRATION WAS 6.5 MG/ML IN 20 MM BTP, 40 MM KCL, PH 7.5. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 185.449 | α = 90 |
b = 79.67 | β = 119.69 |
c = 144.215 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | CCD | ADSC CCD | 2011-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | Australian Synchrotron | MX1 |
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 | 2.15 | 19.67 | 98 | 0.18 | 13.8 | 3.6 | 97252 | 2 |
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 | 2.15 | 19.67 | 97.1 | 0.46 | 2.9 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 1ZCO | 2.15 | 19.65 | 92353 | 4859 | 97.74 | 0.19072 | 0.18859 | 0.23088 | RANDOM | 33.719 |
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] | |
0.02 | 0.13 | -1.05 | 0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.678 |
r_dihedral_angle_4_deg | 18.21 |
r_dihedral_angle_3_deg | 15.08 |
r_dihedral_angle_1_deg | 5.776 |
r_angle_refined_deg | 1.462 |
r_angle_other_deg | 0.784 |
r_chiral_restr | 0.083 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12336 |
Nucleic Acid Atoms | |
Solvent Atoms | 416 |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |