5Q1Y
PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000032a
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 298 | 30% PEG1000, 0.1 M MIB buffer |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.028 | α = 90 |
b = 56.998 | β = 90 |
c = 115.098 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS PILATUS 6M | 2017-04-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.42 | 57.54 | 100 | 0.059 | 0.064 | 0.025 | 0.999 | 12.4 | 6.3 | 65414 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.42 | 1.46 | 100 | 1.5 | 1.664 | 0.711 | 0.512 | 5.4 | 4799 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 5aho | 1.42 | 57.54 | 61823 | 3134 | 99.29 | 0.1771 | 0.1754 | 0.2108 | RANDOM | 24.73 |
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] | |
-0.02 | 0.61 | -0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.336 |
r_sphericity_free | 32.751 |
r_sphericity_bonded | 12.894 |
r_dihedral_angle_3_deg | 11.907 |
r_dihedral_angle_4_deg | 10.462 |
r_dihedral_angle_1_deg | 6.033 |
r_mcangle_it | 2.716 |
r_mcbond_it | 2.066 |
r_mcbond_other | 2.062 |
r_angle_refined_deg | 1.359 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2692 |
Nucleic Acid Atoms | |
Solvent Atoms | 308 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |