4DDD
Crystal structure of an immunogenic protein from ehrlichia chaffeensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | EBS SCREEN JCSG+ H6: 100MM BISTRIS PH 6.5, 17% PEG 10K, 100MM AMMONIUM ACETATE, EHCHA.00493.A.A2 PS01157 AT 18MG/ML; CRYSTAL FOR PHASING WAS SOAKED IN CRYSTALLIZATION BUFFER CONTAINING 1M IODIDE, PH 8.5., VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.71 | α = 90 |
b = 65.44 | β = 90 |
c = 90.97 | 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 | RIGAKU SATURN 944 | RIGAKU VARIMAX | 2011-08-12 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | RIGAKU VARIMAX | 2012-01-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | ||
2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | |||||||
1,2 | 1.9 | 50 | 99 | 0.061 | 0.061 | 21.2 | 5.94 | 30172 | 29858 | -3 | 22.47 |
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) | ||||||||||
1,2 | 1.9 | 1.95 | 91.3 | 0.309 | 0.309 | 3.6 | 2.8 | 2168 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.9 | 45.49 | 30172 | 29858 | 1515 | 99 | 0.161 | 0.161 | 0.159 | 0.188 | RANDOM | 13.57 |
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] | |
-0.07 | 0.11 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.188 |
r_dihedral_angle_4_deg | 16.148 |
r_dihedral_angle_3_deg | 13.122 |
r_dihedral_angle_1_deg | 6.037 |
r_angle_refined_deg | 1.685 |
r_angle_other_deg | 0.962 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2300 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |