9N3N | pdb_00009n3n

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8VEO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629110% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine
Crystal Properties
Matthews coefficientSolvent content
2.7955.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.49α = 90
b = 136.41β = 90
c = 178.02γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0000SPring-8BL45XU

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
12.7546.321000.1740.99510.19.53279956.65
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)
12.752.91001.0520.87229.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE2.7546.321.3632789157799.950.22070.21850.21850.26420.264161.86
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.2236
f_angle_d0.5975
f_chiral_restr0.0451
f_plane_restr0.0041
f_bond_d0.0022
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7346
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms142

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing