2GHI
Crystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MV5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 297 | 29%Peg 3350, 0.2M Li2SO4, 4% Glycerol, and 0.1M BisTris pH 5.5 , VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.015 | α = 69.81 |
b = 70.689 | β = 76.69 |
c = 74.384 | γ = 82.29 |
Symmetry | |
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Space Group | P 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HR | 2006-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E | 1.54 |
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 | 2.2 | 50 | 99.9 | 0.1 | 0.1 | 8 | 5.2 | 56948 | 56948 | 43.6 |
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) | ||||||||||
2.2 | 2.24 | 100 | 0.67 | 0.67 | 1.77 | 4.9 | 2824 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1MV5 | 2.2 | 32.67 | 56088 | 56087 | 857 | 99.06 | 0.20568 | 0.20568 | 0.20448 | 0.28834 | RANDOM | 44.88 |
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] | |
-0.28 | 0.62 | 0.1 | 0.55 | -0.42 | -0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.137 |
r_dihedral_angle_4_deg | 20.632 |
r_dihedral_angle_3_deg | 19.327 |
r_dihedral_angle_1_deg | 7.161 |
r_scangle_it | 3.849 |
r_scbond_it | 2.573 |
r_angle_refined_deg | 1.881 |
r_mcangle_it | 1.6 |
r_mcbond_it | 0.969 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7551 |
Nucleic Acid Atoms | |
Solvent Atoms | 354 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
Coot | model building |