3BKD
High resolution Crystal structure of Transmembrane domain of M2 protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3C9J | Amantandine-bound M2TM; G34A mutant |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 298 | Protein solution: 0.8mM protein, 32mM n-octyl-beta-D-glucopyranoside and 5%v/v xylitol. Reservoir solution: 50mM Tris-Hcl, 500mM MgCl2, 21% PEG 350 MME, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.753 | α = 90 |
b = 56.557 | β = 103.53 |
c = 56.009 | 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 315 | 2001-10-01 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.97853 | NSLS | X25 |
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 | 50 | 94.9 | 0.062 | 22.4 | 3.4 | 15355 | 14567 | 1 | 37.1 |
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 | 2 | 2.05 | 75.1 | 0.305 | 1.9 | 2 | 777 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Amantandine-bound M2TM; G34A mutant | 2.05 | 20 | 14047 | 747 | 99.32 | 0.244 | 0.22158 | 0.21908 | 0.26871 | RANDOM | 31.117 |
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] | |
-0.12 | -0.04 | 2.17 | -2.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.195 |
r_dihedral_angle_4_deg | 19.918 |
r_dihedral_angle_3_deg | 13.966 |
r_dihedral_angle_1_deg | 4.424 |
r_scangle_it | 2.289 |
r_scbond_it | 1.662 |
r_angle_refined_deg | 1.348 |
r_mcangle_it | 1.147 |
r_mcbond_it | 0.887 |
r_xyhbond_nbd_refined | 0.499 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1544 |
Nucleic Acid Atoms | |
Solvent Atoms | 39 |
Heterogen Atoms | 164 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |