3QBP
Crystal structure of fumarase Fum from Mycobacterium marinum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NO9 | pdb entry 3no9, molecule A residues 43 to 393 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID 218662a7, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.1 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 97.88 | ¦Á = 90 |
b = 114.08 | ¦Â = 107.01 |
c = 98.84 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 QUANTUM 315r | 2010-12-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97946 | ALS | 5.0.1 |
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 | 1.85 | 50 | 99.9 | 0.09 | 14.51 | 4.6 | 176835 | 176663 | -3 | 22.3 |
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 | 1.85 | 1.9 | 100 | 0.505 | 3.1 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | pdb entry 3no9, molecule A residues 43 to 393 | 1.85 | 50 | 176519 | 8834 | 99.9 | 0.157 | 0.155 | 0.188 | 17.28 |
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] | |
-0.34 | 0.79 | -0.75 | 1.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.664 |
r_dihedral_angle_4_deg | 17.533 |
r_dihedral_angle_3_deg | 12.559 |
r_dihedral_angle_1_deg | 5.079 |
r_scangle_it | 3.357 |
r_scbond_it | 2 |
r_angle_refined_deg | 1.314 |
r_mcangle_it | 1.203 |
r_mcbond_it | 0.689 |
r_chiral_restr | 0.092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12804 |
Nucleic Acid Atoms | |
Solvent Atoms | 1684 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |