4UHB
Laboratory evolved variant R-C1 of potato epoxide hydrolase StEH1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CJP | PDB ENTRY 2CJP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | PROTEIN IN 30 MM TRIS-HCL, PH 7.4 MIXED 1:1 WITH 0.1 M HEPES PH 7.5, 20 % PEG 10,000. THEN SOAKED IN25% (V/V) GLYCEROL, 75 MM HEPES, PH7.68, PEG 10,000 22.5 % (W/V) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.8 | α = 90 |
b = 96.33 | β = 90 |
c = 121.78 | 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 | ADSC CCD | 2013-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A |
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 | 1.8 | 32.8 | 99.8 | 0.17 | 6.6 | 6.8 | 61576 | 2 |
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 | 1.8 | 1.9 | 99.9 | 0.83 | 2 | 4.7 |
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 2CJP | 1.8 | 32.83 | 57139 | 3006 | 97.63 | 0.19926 | 0.19865 | 0.2109 | RANDOM | 12.172 |
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] | |
-0.27 | 0.96 | -0.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.349 |
r_dihedral_angle_4_deg | 20.247 |
r_dihedral_angle_3_deg | 13.944 |
r_dihedral_angle_1_deg | 5.985 |
r_angle_other_deg | 2.427 |
r_angle_refined_deg | 1.65 |
r_scbond_it | 1.317 |
r_mcangle_it | 1.15 |
r_mcbond_it | 0.742 |
r_mcbond_other | 0.736 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5124 |
Nucleic Acid Atoms | |
Solvent Atoms | 591 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |