7MCJ | pdb_00007mcj

Crystal Structure of S-adenosylmethionine-dependent methyltransferase UmaA from Mycobacterium tuberculosis in complex with compound 8918

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L9U	apo structure, PDB entry 7L9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	287	Optimization condition based on Anatrace/Calibre MCSG1 screen, condition C9: 33% (w/V) PEG 4000, 800mM lithium chloride, 100mM Tris Base/ HCl pH 8.0: MytuD.00149.b.B1.PW38903 at 35mg/ml + 5mM compound 8918: tray 319823 a10, cryo: 20% EG + 5mM compound: puck hyq3-8

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.85	α = 90
b = 100.85	β = 90
c = 49.69	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2021-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.8	50	100	0.054	0.061	0.998	15.85	4.66		52394			40.035

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99.9		0.563	0.648	0.749	2.23	4.124

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	apo structure, PDB entry 7L9U	1.8	43.19	1.98	52371	2091	99.97	0.1901	0.1887	0.19	0.2205	0.22	0	41.85

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.5752
f_angle_d	0.7371
f_chiral_restr	0.0481
f_bond_d	0.0059
f_plane_restr	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4355
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building
Coot	model building

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.