6ZJ1
Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with tetrasaccharide N-glycan fragment 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 | 6ZFA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | 100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 129.414 | α = 90 |
b = 129.414 | β = 90 |
c = 50.201 | 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 EIGER2 XE 16M | 2019-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.95004 | Diamond | I04 |
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 | 1.957 | 112.076 | 50.1 | 0.093 | 0.098 | 0.029 | 0.999 | 15.7 | 11.7 | 17490 |
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 | 1.957 | 2.155 | 11.9 | 1.448 | 1.522 | 0.463 | 0.658 | 1.6 | 10.5 |
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 | 6ZFA | 1.957 | 64.707 | 17488 | 844 | 50.122 | 0.187 | 0.1838 | 0.2524 | 40.367 |
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] | |
-0.063 | -0.032 | -0.063 | 0.205 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.769 |
r_dihedral_angle_3_deg | 15.956 |
r_dihedral_angle_4_deg | 13.486 |
r_dihedral_angle_1_deg | 7.275 |
r_lrange_it | 7.177 |
r_lrange_other | 7.166 |
r_scangle_it | 5.298 |
r_scangle_other | 5.297 |
r_mcangle_other | 4.767 |
r_mcangle_it | 4.758 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2992 |
Nucleic Acid Atoms | |
Solvent Atoms | 133 |
Heterogen Atoms | 109 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
STARANISO | data processing |
REFMAC | phasing |
XDS | data reduction |