2ALW
Golgi alpha-mannosidase II complex with Noeuromycin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HWW | PDB Entry 1HWW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | Tris, PEG 6K, MPD, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 42.97 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 68.502 | ¦Á = 90 |
b = 109.19 | ¦Â = 90 |
c = 138.148 | ¦Ã = 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 | 100 | IMAGE PLATE | MARRESEARCH | Osmic | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 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 | 1.86 | 30 | 99.2 | 0.057 | 29.3 | 5.6 | 88093 | 87388 | 2 | 2 | 13.3 |
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 | 1.86 | 1.9 | 94.4 | 0.31 | 4.55 | 3.8 | 5466 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 1HWW | 1.86 | 26.85 | 2 | 87627 | 85048 | 4298 | 97.1 | 0.159 | 0.141 | 0.141 | 0.181 | RANDOM | 19.9 |
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] | |
-3.87 | 1.86 | 2.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25 |
c_scangle_it | 4.17 |
c_scbond_it | 2.93 |
c_mcangle_it | 2.36 |
c_angle_deg | 1.8 |
c_mcbond_it | 1.75 |
c_improper_angle_d | 1.2 |
c_bond_d | 0.019 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8181 |
Nucleic Acid Atoms | |
Solvent Atoms | 1073 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |