3HPE
Crystal structure of yceI (HP1286) from Helicobacter pylori
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WUB | PDB entry 1WUB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 298 | 0.1M Tris-HCl, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.936 | α = 90 |
b = 61.312 | β = 92.88 |
c = 88.316 | 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 | MARMOSAIC 225 mm CCD | 2009-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8726 | ESRF | ID23-2 |
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 | 2.1 | 50.3 | 99.9 | 0.124 | 10.5 | 6.1 | 19367 | 19367 | 33.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.1 | 2.21 | 99.9 | 0.424 | 4.9 | 6 | 2823 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1WUB | 2.1 | 50.3 | 19367 | 19367 | 1519 | 99.89 | 0.21708 | 0.21708 | 0.21242 | 0.27425 | RANDOM | 7.54 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.35 | 2.06 | -1.27 | -1.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.696 |
r_dihedral_angle_4_deg | 25.502 |
r_dihedral_angle_3_deg | 18.491 |
r_dihedral_angle_1_deg | 6.658 |
r_scangle_it | 3.801 |
r_scbond_it | 2.368 |
r_angle_refined_deg | 1.921 |
r_mcangle_it | 1.217 |
r_mcbond_it | 0.665 |
r_chiral_restr | 0.129 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2632 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |