4Y30

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291.15MgCl, MES buffer pH 6.5, Isopropanol, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.856.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.672α = 90
b = 99.672β = 90
c = 89.252γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.987SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.199.6799.88.3550960

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 DIFFRACTIONTHROUGHOUT2.143.5150960242099.80.18180.17990.2208RANDOM17.88
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]
0.220.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg17.38
r_dihedral_angle_3_deg13.849
r_dihedral_angle_1_deg5.935
r_mcangle_it2.03
r_angle_refined_deg1.386
r_mcbond_it1.176
r_mcbond_other1.176
r_angle_other_deg0.996
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg17.38
r_dihedral_angle_3_deg13.849
r_dihedral_angle_1_deg5.935
r_mcangle_it2.03
r_angle_refined_deg1.386
r_mcbond_it1.176
r_mcbond_other1.176
r_angle_other_deg0.996
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5445
Nucleic Acid Atoms
Solvent Atoms515
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing