Neutron X-ray joint structure of pseudoazurin from Alcaligenes faecalis
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 1PAZ | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | | 293 | 2.8 M deuterated ammonium sulfate |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.61 | 52.9 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 50.168 | α = 90 |
b = 50.168 | β = 90 |
c = 98.292 | γ = 120 |
Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | IMAGE PLATE | LADI III | | 2022-07-19 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | PIXEL | DECTRIS PILATUS3 S 6M | | 2022-10-20 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0000 | Photon Factory | BL-5A |
2 | NUCLEAR REACTOR | JRR-3M BEAMLINE 1G-A | 2.9 | JRR-3M | 1G-A |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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1 | 1.3 | 49.15 | 100 | 0.071 | | | 0.023 | 0.998 | | 16.9 | 10.1 | | 34425 | | | 18.25 |
2 | 1.9 | 100 | 90 | 0.108 | | | 0.074 | 0.988 | | 6.99 | 2.8 | | 9935 | | | 18.25 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.3 | 1.32 | | 0.895 | | | 0.31 | 0.808 | | 2.4 | 9.1 | |
2 | 1.9 | 1.97 | | 0.396 | | | 0.355 | 0.602 | | 2.09 | 1.8 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.5 | 43.45 | | 1.38 | | 22422 | 2272 | 100 | | 0.133 | 0.1288 | 0.1692 | | 45 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 39.7 | | | | 9921 | | 90.04 | | | 0.213 | 0.277 | | |
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] |
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| | | | | |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 18.7808 |
f_angle_d | 1.2129 |
f_chiral_restr | 0.0678 |
f_bond_d | 0.0093 |
f_plane_restr | 0.0091 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 938 |
Nucleic Acid Atoms | |
Solvent Atoms | 72 |
Heterogen Atoms | 6 |
Software
Software |
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Software Name | Purpose |
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DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |