6TRJ
LEDGF/p75 IBD dimer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 (Morpheus Molecular Dimensions condition H11) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.748 | α = 90 |
b = 58.748 | β = 90 |
c = 48.232 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 300K | 2017-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54187 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.3 | 50.88 | 91.8 | 0.043 | 0.047 | 0.999 | 17.65 | 5.467 | 22048 | 21.766 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.3 | 1.38 | 66.5 | 0.827 | 1.001 | 0.498 | 0.96 | 2.615 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | AB INITIO PHASING | THROUGHOUT | 1.3 | 50.88 | 20959 | 1089 | 91.74 | 0.1393 | 0.1373 | 0.1767 | RANDOM | 22.167 |
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] | |
0.05 | 0.02 | 0.05 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.096 |
r_sphericity_free | 25.953 |
r_sphericity_bonded | 13.458 |
r_dihedral_angle_4_deg | 12.178 |
r_dihedral_angle_3_deg | 11.584 |
r_rigid_bond_restr | 3.951 |
r_dihedral_angle_1_deg | 3.862 |
r_angle_refined_deg | 1.518 |
r_angle_other_deg | 1.098 |
r_chiral_restr | 0.08 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 684 |
Nucleic Acid Atoms | |
Solvent Atoms | 115 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Arcimboldo | phasing |