6NT2
type 1 PRMT in complex with the inhibitor GSK3368715
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | SAH and inhibitor were added to PRMT1 to a final concentration of 1.5mM each (3% DMSO). The complex was incubated at 4deg C before crystallization. 1uL protein-ligand complex was mixed with 1 uL of reservoir solution containing 0.3M sodium formate, 0.1M HEPES, 8% PEG 10,000, pH 6.5, and 0.2 uL 30% sodium dextran sulfate Mr=5,000). The droplets were incubated against 500uL reservoir solution for 1-2 days before crystals were observed. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.17 | 61.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 174.15 | α = 90 |
b = 174.15 | β = 90 |
c = 142.35 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | MARRESEARCH | 2013-08-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.0000 | APS | 21-ID-D |
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 | 2.48 | 38.94 | 100 | 0.179 | 0.189 | 0.06 | 0.996 | 12.7 | 9.9 | 77777 |
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 | 2.48 | 2.51 | 100 | 0.961 | 1.013 | 0.319 | 0.81 | 2.7 | 10.1 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.48 | 38.94 | 73795 | 3909 | 99.95 | 0.19183 | 0.19026 | 0.22169 | RANDOM | 22.078 |
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] | |
0.54 | 0.54 | -1.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.506 |
r_dihedral_angle_4_deg | 14.655 |
r_dihedral_angle_3_deg | 13.001 |
r_dihedral_angle_1_deg | 5.938 |
r_long_range_B_refined | 3.087 |
r_long_range_B_other | 3.015 |
r_angle_refined_deg | 1.196 |
r_angle_other_deg | 0.851 |
r_mcangle_it | 0.768 |
r_mcangle_other | 0.768 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10732 |
Nucleic Acid Atoms | |
Solvent Atoms | 664 |
Heterogen Atoms | 354 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |