8X6K | pdb_00008x6k

The X-ray structure of N-terminal catalytic domain of Thermoplasma acidophilum tRNA methyltransferase Trm56 (Ta0931).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YY8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	PEG3350, Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.074	α = 90
b = 110.074	β = 90
c = 57.728	γ = 120

Symmetry
Space Group	P 32 2 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 4M		2022-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

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	98.7	0.051	0.053	0.9990000000000001	30.43	5.3		36948

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	1.91			0.387	0.401	0.97

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 (All)	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	2yy8	1.802	36.03	36939	1847	98.701	0.167	0.1654	0.1768	0.2024	0.2096	RANDOM	30.909

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]
0.005	0.002		0.005		-0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.219
r_dihedral_angle_6_deg	16.747
r_dihedral_angle_3_deg	15.024
r_lrange_other	7.544
r_lrange_it	7.539
r_dihedral_angle_1_deg	6.664
r_scangle_it	6.22
r_scangle_other	6.219
r_scbond_it	4.45
r_scbond_other	4.448
r_mcangle_other	3.777
r_mcangle_it	3.776
r_mcbond_it	2.966
r_mcbond_other	2.966
r_angle_refined_deg	1.7
r_angle_other_deg	0.619
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.238
r_symmetry_xyhbond_nbd_refined	0.235
r_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.184
r_nbd_other	0.16
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2416
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	8

Software

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