22OW | pdb_000022ow

Crystal structure of O-adenosylmethionine-dependent methyltransferase McbD in complex with SAH

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296.15	5 mM SAH under conditions of 0.1 M Tris (pH 8.0), 0.2 M (NH4)2SO4 and 17.2% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.072	α = 90
b = 132.072	β = 90
c = 250.433	γ = 120

Symmetry
Space Group	P 65 2 2

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 EIGER2 S 9M		2024-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.987	SSRF	BL02U1

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	3	39.91	100	0.037	0.052	0.037	0.999	12.6	1.8		26603

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.18	100		0.809	2.9	1.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3	39.91	26602	1330	99.91	0.2	0.1965	0.1963	0.2715	0.2714	74.322

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]
0.904	0.452		0.904		-2.932

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.262
r_dihedral_angle_6_deg	14.121
r_dihedral_angle_2_deg	12.992
r_lrange_it	12.982
r_lrange_other	12.981
r_scangle_it	9.887
r_scangle_other	9.886
r_mcangle_other	7.972
r_mcangle_it	7.971
r_dihedral_angle_1_deg	6.496
r_scbond_it	6.155
r_scbond_other	6.155
r_mcbond_it	5.109
r_mcbond_other	5.108
r_angle_refined_deg	1.445
r_angle_other_deg	0.472
r_symmetry_xyhbond_nbd_refined	0.4
r_symmetry_nbd_refined	0.386
r_nbd_other	0.254
r_nbd_refined	0.234
r_symmetry_nbd_other	0.228
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.182
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.079
r_xyhbond_nbd_other	0.076
r_chiral_restr	0.064
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d
r_dihedral_angle_other_2_deg

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7014
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling