3NA5
Crystal structure of a bacterial phosphoglucomutase, an enzyme important in the virulence of several human pathogens.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FUV | PDB Entry 2FUV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.1 M Bis-Tris, 0.3 M magnesium chloride, 20% PEG 3350,0.1% n-octyl-beta D-gluco-pyranoside , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.466 | α = 90 |
b = 105.792 | β = 90 |
c = 126.797 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 103 | CCD | NOIR-1 | beamline optics | 2010-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0 | ALS | 4.2.2 |
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 | 1.7 | 42.27 | 99.9 | 0.056 | 10.8 | 4.7 | 120749 |
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) | |||||||||||
1.7 | 1.7 | 99.3 | 0.487 | 2.3 | 3.66 |
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 | REFINEMENT | THROUGHOUT | PDB Entry 2FUV | 1.7 | 42.27 | 114594 | 114594 | 6066 | 99.87 | 0.18355 | 0.18176 | 0.2178 | RANDOM | 18.729 |
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 | -0.27 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.737 |
r_dihedral_angle_4_deg | 21.832 |
r_dihedral_angle_3_deg | 11.866 |
r_dihedral_angle_1_deg | 5.69 |
r_scangle_it | 3.264 |
r_scbond_it | 2.055 |
r_angle_refined_deg | 1.456 |
r_mcangle_it | 1.151 |
r_mcbond_it | 0.688 |
r_chiral_restr | 0.124 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8045 |
Nucleic Acid Atoms | |
Solvent Atoms | 1020 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |