5VJU
De Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-bond, Heme B, and Cd(II) ions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 277 | 24% w/v PEG 1500, 70 mM CdCl2, 100 mM Na acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.485 | α = 90 |
b = 25.876 | β = 103.64 |
c = 73.708 | 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 | RIGAKU SATURN 944+ | Osmic VariMax mirror | 2015-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
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 | 2.02 | 71.63 | 97.3 | 0.051 | 0.055 | 0.999 | 25.98 | 6.705 | 10744 | -3 | 25.547 |
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 | 2.02 | 2.07 | 71 | 0.101 | 0.12 | 0.983 | 9.46 | 3.347 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.08 | 71.63 | 9587 | 527 | 98.64 | 0.1869 | 0.1834 | 0.2434 | RANDOM | 31.833 |
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] | |
0.53 | -0.27 | 0.94 | -1.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.432 |
r_dihedral_angle_4_deg | 17.954 |
r_dihedral_angle_3_deg | 15.39 |
r_dihedral_angle_1_deg | 6.322 |
r_angle_refined_deg | 1.782 |
r_angle_other_deg | 1.027 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.007 |
r_gen_planes_other | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1587 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SOLVE | phasing |