8AF4
Room temperature SSX structure of GH11 xylanase from Nectria haematococca (40000 frames)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6Y0H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 5.5 | 293 | For crystallization, the original conditions were modified to obtain microcrystals. Initial crystals obtained from hanging drops under the precipitant condition: 1 M ammonium sulfate, 100 mM sodium citrate pH 5.5 were crushed under a stereomicroscope, using a crystal crusher tool (Hampton research). The reservoir solution was pipetted to the drop and the seed stock was collected by washing the drop with reservoir solution. The seed stock was transferred to a seed bead tube (Molecular Dimensions Ltd., UK), vortexed three times for 30 s each, with an interval of 30 s between each vortex, to get the final seed stock. Protein solution 15 mg/mL, precipitant solution, and seed stock were mixed with a ratio of 1:1:0.5. The mixture was vortexed for 30 s in ten-minute intervals. After 30 min, the microcrystals were centrifuged at 200 rpm and the supernatant was replaced with a precipitant solution. Applying the same protocol, microcrystals were obtained under two precipitant conditions i.e. Precipitant 1: 1M (NH4)2SO4, 100 mM sodium citrate pH 5.5, and Precipitant 2: 200 mM (NH4)2SO4, 100 mM sodium citrate pH 5.5 and 20% PEG 6000. Microcrystals obtained under both precipitant conditions were tested for diffraction data collection |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.55 | α = 90 |
b = 38.85 | β = 91 |
c = 53.57 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 295 | PIXEL | DECTRIS PILATUS 6M | 2019-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, DESY BEAMLINE P11 | 1.0332 | PETRA III, DESY | P11 |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | TapeDrive | injection |
Injection | |||||||
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
1 | TapeDrive | 1 |
Data Reduction | |||
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Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 40000 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 1.51 | 17.16 | 98.75 | 0.987 | 0.1342 | 5.83 | 432 | 25916 | 19.51 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.51 | 1.54 | 87.48 | 0.152 | 2.49 | 0.55 |
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 (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6Y0H | 1.51 | 17.16 | 1.33 | 25569 | 1985 | 97.33 | 0.1541 | 0.1516 | 0.1831 | 23.58 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.2582 |
f_angle_d | 1.0591 |
f_chiral_restr | 0.0618 |
f_bond_d | 0.0094 |
f_plane_restr | 0.0063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1459 |
Nucleic Acid Atoms | |
Solvent Atoms | 220 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHENIX | phasing |