8G2F

Crystal Structure of PRMT3 with Compound II710


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29120% PEG3350, 0.3 M Sodium Formate
Crystal Properties
Matthews coefficientSolvent content
2.8657.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.733α = 90
b = 70.733β = 90
c = 175.262γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.065097.40.0918.910.427517
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.181.60.8410.9151.78.1

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 REPLACEMENTTHROUGHOUT2.0648.1426354108897.060.208830.206950.25598RANDOM54.369
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]
3.093.09-6.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.746
r_dihedral_angle_4_deg23.539
r_dihedral_angle_3_deg16.664
r_long_range_B_other7.718
r_long_range_B_refined7.712
r_dihedral_angle_1_deg7.525
r_scangle_other6.464
r_mcangle_it5.419
r_mcangle_other5.419
r_scbond_it4.796
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.746
r_dihedral_angle_4_deg23.539
r_dihedral_angle_3_deg16.664
r_long_range_B_other7.718
r_long_range_B_refined7.712
r_dihedral_angle_1_deg7.525
r_scangle_other6.464
r_mcangle_it5.419
r_mcangle_other5.419
r_scbond_it4.796
r_scbond_other4.794
r_mcbond_it4.233
r_mcbond_other4.233
r_angle_refined_deg1.358
r_angle_other_deg1.243
r_chiral_restr0.057
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2338
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms33

Software

Software
Software NamePurpose
HKL-3000data scaling
PHASERphasing
REFMACrefinement
HKL-3000data reduction