3PM6
Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ISV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 289 | 23.4 mg/mL CoimA.00345.a.A1 PS00465 against ProPlex screen condition E11, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, soaked into 1 M NaI, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, 20% ethylene glycol, crystal tracking ID 206915e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 45.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.91 | α = 90 |
b = 77.77 | β = 93.71 |
c = 68.32 | γ = 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 | RIGAKU SATURN 944 | Osmic VariMax HF | 2010-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 2.2 | 50 | 97.5 | 0.104 | 12.96 | 7.3 | 30826 | 30048 | -3 | 34.628 |
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 | 2.2 | 2.26 | 82.8 | 0.478 | 3.7 | 6 | 2254 |
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 | SAD WITH MR | THROUGHOUT | 2isv | 2.2 | 50 | 30008 | 1505 | 97.35 | 0.1998 | 0.1978 | 0.2369 | RANDOM | 27.6569 |
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] | |
-0.5 | 1.32 | -0.76 | 1.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.496 |
r_dihedral_angle_4_deg | 22.928 |
r_dihedral_angle_3_deg | 14.998 |
r_dihedral_angle_1_deg | 5.506 |
r_scangle_it | 3.425 |
r_scbond_it | 2.11 |
r_angle_refined_deg | 1.428 |
r_mcangle_it | 1.298 |
r_mcbond_it | 0.708 |
r_chiral_restr | 0.094 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4114 |
Nucleic Acid Atoms | |
Solvent Atoms | 247 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |