4LX4
Crystal Structure Determination of Pseudomonas stutzeri endoglucanase Cel5A using a Twinned Data Set
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4EE9 | PDB ENTRY 4EE9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | Ps_Cel5A (27 microM) in 50 mM sodium phosphate pH 7.0, was mixed 1:1 with well buffer (100 mM tris pH 5.9 with 22.5 % v/v polyethylene glycol 600) using the hanging drop method with 500 uL well buffer in the well of the crystallization tray. Crystals obtained by this method were soaked 1 hour in 100 mM Tris pH 5.9 with 30% v/v polyethylene glycol 600., VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.39 | α = 90 |
b = 82.9 | β = 92.08 |
c = 104.74 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | ADSC QUANTUM 315r | 2012-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.979639 | ESRF | BM30A |
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 | 1.556 | 48.279 | 91.6 | 0.076 | 0.07 | 17.9 | 7.1 | 157788 | 157658 | -3 | 20.1 |
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 | 1.56 | 1.6 | 97.7 | 0.339 | 0.314 | 5.9 | 7.07 | 12421 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 4EE9 | 1.556 | 48.279 | 1.36 | 157658 | 157658 | 8444 | 91.58 | 0.2236 | 0.2196 | 0.2371 | INHERITED | 12.4 |
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 |
f_dihedral_angle_d | 13.084 |
f_angle_d | 1.177 |
f_chiral_restr | 0.08 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10315 |
Nucleic Acid Atoms | |
Solvent Atoms | 1131 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |