1OFQ
CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH MANGANESE(II)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HFB | PDB ENTRY 1HFB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 277 | TRIS PH 7.5-9.0 10 MM 20% PEG3400, 2.4 EQUIV. MN, 13-17MG/ML DAHPS, 4 DEGREE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.731 | α = 90 |
b = 105.731 | β = 90 |
c = 268.782 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 105 | CCD | MARRESEARCH | MIRRORS | 2001-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 |
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 | 2.4 | 19.8 | 99.5 | 0.046 | 26.5 | 8.8 | 68895 | 48.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 2.5 | 100 | 0.199 | 13.5 | 6.1 |
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 | PDB ENTRY 1HFB | 2.7 | 19.98 | 46957 | 1375 | 96.6 | 0.221 | 0.221 | 0.245 | RANDOM | 44.5 |
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] | |
4.27 | 5.97 | 4.27 | -8.53 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.7 |
c_scangle_it | 2.12 |
c_mcangle_it | 1.59 |
c_scbond_it | 1.41 |
c_angle_deg | 1.2 |
c_mcbond_it | 0.95 |
c_improper_angle_d | 0.79 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10283 |
Nucleic Acid Atoms | |
Solvent Atoms | 285 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |