1T0A
Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GX1 | PDB entry 1GX1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 295 | formate, glycerol, TRIS, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.6 | 65.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.088 | α = 90 |
b = 117.088 | β = 90 |
c = 108.937 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | BRUKER SMART 6000 | Montel mirrors | 2003-07-17 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | BRANDEIS - B4 | beam focused by a toroidal mirror | 2003-07-29 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR591 | 1.5418 | ||
2 | SYNCHROTRON | NSLS BEAMLINE X12C | .97911 | NSLS | X12C |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.6 | 81.65 | 0.081 | 0.081 | 55.7 | 14.5 | 99854 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.6 | 1.66 | 100 | 0.5 | 0.5 | 5.9 | 13.1 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1GX1 | 1.6 | 29.8 | 99854 | 94783 | 4986 | 99.97 | 0.17526 | 0.17434 | 0.19307 | RANDOM | 15.215 |
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] | |
-0.17 | -0.17 | 0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.808 |
r_scangle_it | 4.55 |
r_scbond_it | 2.87 |
r_mcangle_it | 1.774 |
r_angle_refined_deg | 1.603 |
r_mcbond_it | 1.005 |
r_angle_other_deg | 0.884 |
r_symmetry_hbond_refined | 0.334 |
r_nbd_other | 0.254 |
r_nbd_refined | 0.23 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3555 |
Nucleic Acid Atoms | |
Solvent Atoms | 583 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |