5V33
R. sphaeroides photosythetic reaction center mutant - Residue L223, Ser to Trp - Room Temperature Structure Solved on X-ray Transparent Microfluidic Chip
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROFLUIDIC | 7.8 | 293 | Crystals were grown in microfluidic wells. LCPs were formulated by overlaying ~40 nl of protein solution over ~10 nl of solid monoolein. LCPs formed by diffusion during a 4 hour incubation. Precipitants were then introduced to the crystallization well, and crystals were observed after 3 days. Crystals were grown at 15-20 mg/mL protein concentration (in 10 mM Tris pH 7.8, 280 mM NaCl, 0.05% LDAO) with a precipitant of 1 M HEPES pH 7.5, 1.15 M (NH4)2(SO4) and 14-15 %w/v Jeffamine M-600. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.44 | 64.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.332 | α = 90 |
b = 102.332 | β = 90 |
c = 240.333 | γ = 90 |
Symmetry | |
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Space Group | P 42 21 2 |
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 | 298 | PIXEL | DECTRIS PILATUS 6M | 2016-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.000 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 3.5 | 50 | 92 | 0.29 | 0.322 | 0.132 | 2.9 | 5.4 | 15671 | 54.65 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.5 | 3.56 | 94.6 | 0.72 | 0.793 | 0.317 | 0.618 | 5.4 | 784 |
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 | FREE R-VALUE | 4TQQ | 3.487 | 47.076 | 14260 | 1435 | 83.65 | 0.2246 | 0.2205 | 0.2616 | Random selection | 45.5477 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.053 |
f_angle_d | 0.702 |
f_chiral_restr | 0.025 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6476 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 443 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |
DENZO | data reduction |
SCALEPACK | data scaling |