6SAZ
Cleaved human fetuin-b in complex with crayfish astacin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6HT9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.46 | 64.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.7 | α = 90 |
b = 90.7 | β = 90 |
c = 283.9 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 PILATUS3 6M | 2018-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 1.0032 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 3 | 78.5 | 99.7 | 0.184 | 0.195 | 0.996 | 11.1 | 9.2 | 26287 | 70.5 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3 | 3.18 | 98.9 | 1.565 | 1.66 | 0.626 | 8.9 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6HT9 | 3 | 78.5 | 25577 | 708 | 99.7 | 0.185 | 0.247 | Random | 82.4 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6832 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms | 142 |
Software
Software | |
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Software Name | Purpose |
BUSTER-TNT | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |