5VJS
De Novo Photosynthetic Reaction Center Protein Equipped with Heme B, a synthetic Zn porphyrin, and Zn(II) cations
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 277 | 3.4 M NaCl, 100 mM Na acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.749 | α = 90 |
b = 43.749 | β = 90 |
c = 245.737 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | 100 | CCD | ADSC QUANTUM 270 | Oxford Danfysik toroidal focusing mirror | 2013-11-20 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.0781, 1.2824, 1.2831 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 61.43 | 99.4 | 0.085 | 0.091 | 0.999 | 16.8 | 7.603 | 17105 | -3 | 37.05 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2 | 2.05 | 98.8 | 0.97 | 1.041 | 0.888 | 2.52 | 7.409 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2 | 61.43 | 16280 | 830 | 99.33 | 0.2366 | 0.2345 | 0.2779 | RANDOM | 40.772 |
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] | |
2.38 | 2.38 | -4.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.585 |
r_dihedral_angle_4_deg | 16.471 |
r_dihedral_angle_3_deg | 16.185 |
r_dihedral_angle_1_deg | 4.947 |
r_angle_refined_deg | 1.829 |
r_angle_other_deg | 1.095 |
r_chiral_restr | 0.114 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1585 |
Nucleic Acid Atoms | |
Solvent Atoms | 39 |
Heterogen Atoms | 88 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
AutoSol | phasing |
PDB_EXTRACT | data extraction |