8B1N | pdb_00008b1n

Crystal structure of TrmD-Tm1570 from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WYR	5WYR, 3DCM
experimental model	PDB	3DCM	5WYR, 3DCM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein sample: 5.7 mg/mL TrmD-Tm1570 in 50 mM HEPES buffer pH 7.4, 300 mM NaCl, 5% glycerol, with addition of 3 mM SAM, 0.1% DDM and 3000x diluted seeds stock. Reservoir solution: 0.2 M MgCl2, 0.1 M Tris pH 7.0, 10% PEG 8000.

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.78	α = 90
b = 199.56	β = 90
c = 56.7	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 2M		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	49.3	99.9	0.138	0.999	13.68	8.81		75191			33.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12	99.4		1.523	0.616	1.43	8.69

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5WYR, 3DCM	2	48.92	1.34	75168	2100	99.85	0.1703	0.1691	0.2088	0.1817	42.87

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	17.2208
f_angle_d	0.8241
f_chiral_restr	0.0531
f_bond_d	0.0065
f_plane_restr	0.0043

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6679
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	162

Software

Software
Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	model building
Coot	model building
PHENIX	refinement