3LQ0
Zymogen structure of crayfish astacin metallopeptidase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AST | PDB ENTRY 1AST |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 277 | For crystallization, reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x2-well MRC plates (Innovadyne) by a Cartesian (Genomic Solutions) nanodrop robot at the High-Throughput Crystallography Platform of the Barcelona Science Park. Best crystals appeared in a Bruker steady-temperature crystal farm at 4C with protein solution (10 mg/mL in 50mM AMPSO pH9.0) and 20% PEG 8000, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6 as reservoir solution. These conditions were efficiently scaled up to the microliter range with 24-well Cryschem crystallization dishes (Hampton Research). Crystals were cryo-protected with 16% PEG 8000, 20% glycerol, 0.1M (NH4)2SO4, 0.01M MgCl2, 0.05M MES pH5.6. , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.91 | α = 90 |
b = 63.37 | β = 90 |
c = 69.19 | γ = 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 | CCD | MAR CCD 165 mm | 2009-10-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.873 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.45 | 46.73 | 99.8 | 0.044 | 0.044 | 27.3 | 7.1 | 44316 | 44227 | 1.44 | 2 | 14.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.45 | 1.54 | 98.9 | 0.474 | 0.474 | 3.8 | 6.2 | 6285 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 1AST | 1.45 | 41.92 | 44284 | 43398 | 768 | 99.73 | 0.15218 | 0.15218 | 0.15169 | 0.18046 | RANDOM | 7.029 |
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] | |
-0.69 | -0.87 | 1.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.382 |
r_dihedral_angle_4_deg | 19.977 |
r_dihedral_angle_3_deg | 12.504 |
r_dihedral_angle_1_deg | 6.213 |
r_sphericity_free | 5.332 |
r_scangle_it | 3.675 |
r_scbond_it | 2.694 |
r_sphericity_bonded | 2.085 |
r_mcangle_it | 1.791 |
r_angle_refined_deg | 1.532 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1859 |
Nucleic Acid Atoms | |
Solvent Atoms | 298 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
ProDC | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |