7L5M
Crystal Structure of the DiB-RM-split Protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QWD | PDB entry 1QWD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 294 | 1.6 M ammonium sulfate, 0.1 M MES, pH 4.5, supplemented with 0.5% n-Dodecyl-b-D-maltoside |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.146 | α = 90 |
b = 57.146 | β = 90 |
c = 138.63 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | MARMOSAIC 225 mm CCD | 2020-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | Rpim I (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 | |||||||
1 | 2.33 | 46.21 | 100 | 0.087 | 0.03 | 10.9 | 8 | 10501 | 49.674 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.33 | 2.37 | 100 | 0.697 | 0.286 | 1.8 | 5.3 |
Refinement
Statistics | |||||||||||||||||||
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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 1QWD | 2.33 | 44.13 | 9939 | 501 | 99.9 | 0.2404 | 0.2385 | 0.2787 | RANDOM | 55.752 |
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 | 0.53 | -1.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.49 |
r_dihedral_angle_4_deg | 20.018 |
r_dihedral_angle_3_deg | 16.321 |
r_dihedral_angle_1_deg | 8.139 |
r_mcangle_it | 6.253 |
r_mcbond_it | 4.349 |
r_mcbond_other | 4.348 |
r_angle_other_deg | 2.344 |
r_angle_refined_deg | 1.547 |
r_chiral_restr | 0.069 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1218 |
Nucleic Acid Atoms | |
Solvent Atoms | 12 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOLREP | phasing |
xia2 | data scaling |
PDB_EXTRACT | data extraction |
xia2 | data reduction |