5M82
Three-dimensional structure of the photoproduct state of GAF3 from Slr1393 of Synechocystis sp. PCC6803
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M85 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 277 | 0.1 M NaCl, 0.1 M CAPSO pH 9.5, 0.175 M LiSO4, 14% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.286 | α = 90 |
b = 75.286 | β = 90 |
c = 71.38 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | PIXEL | DECTRIS PILATUS 6M-F | KB mirrors | 2015-10-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.976252 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.86 | 65.2 | 94.4 | 0.027 | 1 | 25.79 | 3.89 | 18191 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.86 | 1.98 | 78.9 | 0.92 | 3.37 | 3.07 |
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 | 5M85 | 1.86 | 65.2 | 17263 | 921 | 94.33 | 0.19596 | 0.1941 | 0.22872 | RANDOM | 38.426 |
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] | |
0.53 | 0.26 | 0.53 | -1.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.767 |
r_dihedral_angle_4_deg | 15.857 |
r_dihedral_angle_3_deg | 12.798 |
r_long_range_B_other | 8.055 |
r_long_range_B_refined | 8.03 |
r_dihedral_angle_1_deg | 6.737 |
r_scangle_other | 6.544 |
r_scbond_it | 4.414 |
r_scbond_other | 4.411 |
r_mcangle_it | 4.394 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1304 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |