9MG6 | pdb_00009mg6

Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase variant, Abd1-K163R-K311R-F387Y-Y416F, in complex with sinefungin and GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9MG4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52922 M Ammonium Sulphate, 1.8% Ethylene Glycol, 100 mM Tris-HCl, 10 mM Tris(2-carboxyethl)phosphine hydrochloride
Crystal Properties
Matthews coefficientSolvent content
4.4772.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.779α = 90
b = 201.17β = 90
c = 160.532γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.92NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.7317.9999.30.1940.2160.0930.9836.85.248851
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.732.8297.30.8010.8860.3750.7195.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.817.9843152226999.420.179910.178060.18540.215230.2179RANDOM33.183
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]
0.960.63-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.169
r_dihedral_angle_2_deg9.175
r_long_range_B_refined8.204
r_long_range_B_other8.163
r_dihedral_angle_1_deg6.218
r_scangle_other5.656
r_mcangle_other3.93
r_mcangle_it3.929
r_scbond_it3.446
r_scbond_other3.407
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.169
r_dihedral_angle_2_deg9.175
r_long_range_B_refined8.204
r_long_range_B_other8.163
r_dihedral_angle_1_deg6.218
r_scangle_other5.656
r_mcangle_other3.93
r_mcangle_it3.929
r_scbond_it3.446
r_scbond_other3.407
r_mcbond_it2.351
r_mcbond_other2.347
r_angle_refined_deg1.494
r_angle_other_deg0.527
r_chiral_restr0.068
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms7163
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing