3SID
Crystal structure of oxidized Symerythrin from Cyanophora paradoxa, azide adduct at 50% occupancy
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QHB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 279 | 25% PEG 3350, 0.1M BisTris, 0.35M NH4Cl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.009 | α = 90 |
b = 82.009 | β = 90 |
c = 46.44 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 315r | 2011-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97650 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.4 | 30.74 | 100 | 0.074 | 18.9 | 12.2 | 68857 | 68857 | 2 | 2 | 13.96 |
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 | 1.4 | 1.48 | 100 | 0.441 | 0.441 | 5.6 | 12 | 10086 |
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 | THROUGHOUT | 3QHB | 1.4 | 30.74 | 65332 | 3484 | 99.96 | 0.11727 | 0.11517 | 0.15618 | RANDOM | 12.676 |
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] | |
-0.74 | -0.37 | -0.74 | 1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.072 |
r_dihedral_angle_4_deg | 17.965 |
r_dihedral_angle_3_deg | 13.672 |
r_sphericity_free | 13.515 |
r_sphericity_bonded | 9.286 |
r_scangle_it | 6.801 |
r_dihedral_angle_1_deg | 4.832 |
r_scbond_it | 4.802 |
r_mcangle_it | 3.304 |
r_mcbond_it | 2.386 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2730 |
Nucleic Acid Atoms | |
Solvent Atoms | 562 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHENIX | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | phasing |