6NT2

type 1 PRMT in complex with the inhibitor GSK3368715


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291SAH 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
Matthews coefficientSolvent content
3.1761.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.15α = 90
b = 174.15β = 90
c = 142.35γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0000APS21-ID-D

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4838.941000.1790.1890.060.99612.79.977777
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
12.482.511000.9611.0130.3190.812.710.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.4838.9473795390999.950.191830.190260.22169RANDOM22.078
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]
0.540.54-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg14.655
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg5.938
r_long_range_B_refined3.087
r_long_range_B_other3.015
r_angle_refined_deg1.196
r_angle_other_deg0.851
r_mcangle_it0.768
r_mcangle_other0.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg14.655
r_dihedral_angle_3_deg13.001
r_dihedral_angle_1_deg5.938
r_long_range_B_refined3.087
r_long_range_B_other3.015
r_angle_refined_deg1.196
r_angle_other_deg0.851
r_mcangle_it0.768
r_mcangle_other0.768
r_scangle_other0.595
r_mcbond_it0.41
r_mcbond_other0.41
r_scbond_it0.326
r_scbond_other0.324
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10732
Nucleic Acid Atoms
Solvent Atoms664
Heterogen Atoms354

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing