5NH8
Crystal structure of xylose isomerase from Piromyces E2 in complex with two Ca2+ ions and xylose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5NH5 | D_1200004044 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 294 | 13-15 % PEG3350, 10 mM CaCl2, 0.1 M Hepes pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 78.764 | ¦Á = 115.41 |
b = 79.337 | ¦Â = 89.91 |
c = 91.926 | ¦Ã = 117.16 |
Symmetry | |
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Space Group | P 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 | 110 | IMAGE PLATE | MARRESEARCH | 2015-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 1.86 | 46.7 | 92.6 | 0.09 | 0.071 | 0.995 | 10.6 | 4 | 136386 | 9.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.86 | 1.89 | 75.7 | 0.488 | 0.384 | 0.602 | 2.1 | 3.2 |
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 | D_1200004044 | 1.86 | 46.7 | 129514 | 6829 | 93.67 | 0.17712 | 0.17585 | 0.20136 | RANDOM | 20.21 |
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] | |
-0.19 | -0.11 | 0.07 | 0.03 | 0.07 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.041 |
r_dihedral_angle_3_deg | 13.042 |
r_dihedral_angle_4_deg | 12.574 |
r_dihedral_angle_1_deg | 5.684 |
r_long_range_B_refined | 4.9 |
r_long_range_B_other | 4.554 |
r_scangle_other | 1.522 |
r_angle_refined_deg | 1.238 |
r_mcangle_it | 1.162 |
r_mcangle_other | 1.162 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13876 |
Nucleic Acid Atoms | |
Solvent Atoms | 1620 |
Heterogen Atoms | 160 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |