2EWE
Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AIR | pectate lyase C, PDB entry 1AIR, with arg 218 omitted |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 277 | Grown in 1.0 M ammonium sulfate, 50 mM HEPES. VAPOR DIFFUSION, SITTING DROP, temperature 277K. Crystals then transferred to a solution at pH 9.5 containing cryogenic agents, 7 mM calcium and 50mM penta-galacturonopyranose, and left to soak for 30 hours. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.54 | 65.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.14 | α = 90 |
b = 78.32 | β = 90 |
c = 94.43 | 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 | 103 | IMAGE PLATE | MARRESEARCH | 1996-12-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.08 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.15 | 23.76 | 95.9 | 0.031 | 11.8 | 28523 | 28523 | 22.9 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | pectate lyase C, PDB entry 1AIR, with arg 218 omitted | 2.2 | 10 | 2 | 26662 | 26512 | 2638 | 96.5 | 0.186 | 0.233 | random | 13.4 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_angle_deg | 1.54 |
x_improper_angle_d | 1.17 |
x_bond_d | 0.0006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2646 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
X-PLOR | phasing |