5H5D

The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C77 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 M NaCl, 0.1 M Tris-HCl (pH 8.5), 38% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.727.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.527α = 90
b = 57.77β = 106.46
c = 43.153γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.979SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.75095.40.111.52.65087
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)
12.72.888.10.3140.8161.92

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5C772.750460823495.070.232160.229550.28217RANDOM57.406
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]
-4.27-0.857.41-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.501
r_dihedral_angle_3_deg13.702
r_dihedral_angle_4_deg12.579
r_long_range_B_refined7.256
r_long_range_B_other7.254
r_scangle_other5.642
r_dihedral_angle_1_deg5.575
r_mcangle_it4.781
r_mcangle_other4.779
r_scbond_it3.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.501
r_dihedral_angle_3_deg13.702
r_dihedral_angle_4_deg12.579
r_long_range_B_refined7.256
r_long_range_B_other7.254
r_scangle_other5.642
r_dihedral_angle_1_deg5.575
r_mcangle_it4.781
r_mcangle_other4.779
r_scbond_it3.764
r_scbond_other3.761
r_mcbond_it3.23
r_mcbond_other3.215
r_angle_refined_deg1.435
r_angle_other_deg0.967
r_chiral_restr0.066
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
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 Atoms1487
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms20

Software

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