6V0O
PRMT5 bound to the PBM peptide from pICln
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.4 | 281 | 30% PEG 3350 200 mM ammonium sulfate 0.05% w/v dodecyl-maltoside |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.76 | 55.5 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 100.01 | α = 90 |
b = 136.4 | β = 90 |
c = 179.77 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2017-04-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.98 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.86 | 44.94 | 98.1 | 0.13 | 0.997 | 8.37 | 3.7 | 28182 | 112.67 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.86 | 2.88 | 97.1 | 2.02 | 0.481 | 0.62 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4GQB | 2.86 | 44.94 | 28182 | 1410 | 97.9 | 0.213 | 0.211 | 0.247 | RANDOM | 115.75 |
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] | |
-26.0429 | -25.4519 | 51.4948 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 20.82 |
t_omega_torsion | 3.07 |
t_angle_deg | 1.18 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7465 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 50 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |