6ZDK
Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES and hexatungstotellurate(VI) TEW
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6ZDF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 292 | 100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 53.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.968 | α = 90 |
b = 128.968 | β = 90 |
c = 48.791 | γ = 120 |
Symmetry | |
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Space Group | P 62 |
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 | PIXEL | DECTRIS PILATUS 6M | 2018-01-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97625 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2 | 64.48 | 99.6 | 0.126 | 0.149 | 0.078 | 0.992 | 6.2 | 3.5 | 31607 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2 | 2.05 | 98.3 | 0.739 | 0.869 | 0.45 | 0.411 | 1.5 | 3.5 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6ZDF | 2 | 64.48 | 31481 | 1554 | 99.592 | 0.198 | 0.1956 | 0.235 | 32.842 |
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] | |
-1.779 | -0.89 | -1.779 | 5.772 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.789 |
r_dihedral_angle_4_deg | 18.755 |
r_dihedral_angle_3_deg | 15.88 |
r_dihedral_angle_1_deg | 6.13 |
r_lrange_it | 5.317 |
r_lrange_other | 5.29 |
r_scangle_it | 4.459 |
r_scangle_other | 3.617 |
r_scbond_it | 3.245 |
r_mcangle_other | 2.798 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2986 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 109 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |