8G2H

Crystal Structure of PRMT4 with Compound YD1113


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U4X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine
Crystal Properties
Matthews coefficientSolvent content
3.2662.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.215α = 90
b = 84.215β = 90
c = 130.426γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-06-11MSINGLE 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
11.49501000.0650.99812.68.287534
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)
11.491.521000.9450.7528.1

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 REPLACEMENTTHROUGHOUT1.4948.6685796168399.70.171470.171340.17745RANDOM19.547
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]
0.210.110.21-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg18.723
r_dihedral_angle_3_deg12.683
r_dihedral_angle_1_deg6.331
r_long_range_B_refined5.255
r_long_range_B_other4.914
r_scangle_other3.71
r_scbond_it2.41
r_scbond_other2.409
r_mcangle_it2.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg18.723
r_dihedral_angle_3_deg12.683
r_dihedral_angle_1_deg6.331
r_long_range_B_refined5.255
r_long_range_B_other4.914
r_scangle_other3.71
r_scbond_it2.41
r_scbond_other2.409
r_mcangle_it2.064
r_mcangle_other2.063
r_angle_refined_deg1.47
r_angle_other_deg1.448
r_mcbond_it1.391
r_mcbond_other1.391
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms2652
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms50

Software

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