2W88
Plastocyanin variant with N-terminal Methionine - open structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CVB | PDB ENTRY 3CVB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1 M ZINC ACETATE, 0.4 M SODIUM ACETATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.45 | 81 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 127.7 | ¦Á = 90 |
b = 127.7 | ¦Â = 90 |
c = 94.99 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 1 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 | RIGAKU IMAGING PLATE | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 |
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 | 2.89 | 47.78 | 99.8 | 0.17 | 4.3 | 7.5 | 19857 | -3 | 54.38 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.89 | 3.05 | 98.4 | 0.58 | 1.3 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 3CVB | 2.89 | 110.43 | 18824 | 1012 | 99.76 | 0.19578 | 0.19433 | 0.22285 | RANDOM | 29.099 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.1 | 0.05 | 0.1 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.592 |
r_dihedral_angle_4_deg | 21.273 |
r_dihedral_angle_3_deg | 18.118 |
r_dihedral_angle_1_deg | 6.249 |
r_scangle_it | 2.204 |
r_scbond_it | 1.446 |
r_angle_refined_deg | 1.351 |
r_mcangle_it | 0.771 |
r_mcbond_it | 0.404 |
r_chiral_restr | 0.087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2439 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |