6SK4 | pdb_00006sk4

Methyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SJ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	100 mM TRIS, 28% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.4	α = 90
b = 73.1	β = 113.36
c = 89.76	γ = 90

Symmetry
Space Group	P 1 21 1

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 16M		2019-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	30	97.2	0.071	0.997	8.1	3.1		139692

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)	Redundancy	Number Unique Reflections (All)
1	1.55	1.65			0.557	0.823	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	6SJ8	1.55	30	132691	6984	97.31	0.2194	0.2095	0.22	0.2433	0.26	RANDOM	21.902

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]
-3.13		1.15	-1.75		2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.596
r_dihedral_angle_4_deg	15.966
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	6.168
r_angle_other_deg	1.286
r_angle_refined_deg	1.276
r_rigid_bond_restr	0.547
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.596
r_dihedral_angle_4_deg	15.966
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	6.168
r_angle_other_deg	1.286
r_angle_refined_deg	1.276
r_rigid_bond_restr	0.547
r_chiral_restr	0.058
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9228
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.