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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9MG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	2 M Ammonium Sulphate, 1.8% Ethylene Glycol, 100 mM Tris-HCl, 10 mM Tris(2-carboxyethl)phosphine hydrochloride

Crystal Properties
Matthews coefficient	Solvent content
4.47	72.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.779	α = 90
b = 201.17	β = 90
c = 160.532	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2023-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92	NSLS-II	17-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.73	17.99	99.3	0.194	0.216	0.093	0.983	6.8	5.2		48851

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)	Redundancy	Number Unique Reflections (All)
1	2.73	2.82		97.3	0.801	0.886	0.375	0.719		5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	17.98	43152	2269	99.42	0.17991	0.17806	0.1854	0.21523	0.2179	RANDOM	33.183

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]
0.96			0.63		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.169
r_dihedral_angle_2_deg	9.175
r_long_range_B_refined	8.204
r_long_range_B_other	8.163
r_dihedral_angle_1_deg	6.218
r_scangle_other	5.656
r_mcangle_other	3.93
r_mcangle_it	3.929
r_scbond_it	3.446
r_scbond_other	3.407
r_mcbond_it	2.351
r_mcbond_other	2.347
r_angle_refined_deg	1.494
r_angle_other_deg	0.527
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	7163
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	258

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing