5A29
Family 2 Pectate Lyase from Vibrio vulnificus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | CRYSTALS OF VVPL2 DEVELOPED VIA HANGING DROP VAPOUR DIFFUSION METHOD AT A PROTEIN CONCENTRATION OF 15 MG/ML BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF 16% (W/V) POLYETHYLENE GLYCOL 3,350, 0.14 M NA/K TARTRATE, AND 0.1 M HEPES (PH 7.0) AT 19 DEGREES CELSIUS. CRYSTALS WERE CRYOPROTECTED BY BRIEF CRYSTAL IMMERSION INTO A SOLUTION OF THE RESERVOIR SOLUTION SUPPLEMENTED WITH 25% ETHYLENE GLYCOL, AND SUBSEQUENTLY FROZEN IN A LIQUID NITROGEN STREAM PRIOR TO DIFFRACTION EXPERIMENTS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.102 | α = 90 |
b = 141.102 | β = 90 |
c = 72.426 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | ADSC QUANTUM 315r | MIRRORS RH COATED | 2013-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.9 | 122 | 99.8 | 0.1 | 29.1 | 4.8 | 64624 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.95 | 100 | 0.42 | 4.6 | 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2V8J | 1.9 | 122.2 | 61132 | 3266 | 99.59 | 0.1579 | 0.15585 | 0.19678 | RANDOM | 27.831 |
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] | |
-0.58 | -0.29 | -0.58 | 1.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.292 |
r_dihedral_angle_4_deg | 16.993 |
r_dihedral_angle_3_deg | 13.36 |
r_dihedral_angle_1_deg | 6.696 |
r_scbond_it | 4.261 |
r_mcangle_it | 3.681 |
r_mcbond_it | 2.97 |
r_angle_refined_deg | 1.907 |
r_chiral_restr | 0.164 |
r_bond_refined_d | 0.02 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4526 |
Nucleic Acid Atoms | |
Solvent Atoms | 498 |
Heterogen Atoms | 79 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |