8X4I

Crystal structure of the D117A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8X3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.4	293	0.2 M Zinc Acetate Dihydrate, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.92	α = 90
b = 124.92	β = 90
c = 36.81	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2022-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	3.3	62.54	93.2	0.164	0.188	0.091	0.967	9.1	4.3		9013

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.57		87.2	0.513	0.586	0.281	0.875		4.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.3	62.54	4330	448	92.56	0.20993	0.20102	0.28654	RANDOM	128.649

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]
-1.5	-0.75		-1.5		4.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.478
r_long_range_B_refined	14.003
r_long_range_B_other	14.001
r_dihedral_angle_1_deg	9.511
r_mcangle_it	8.928
r_mcangle_other	8.925
r_scangle_other	8.465
r_dihedral_angle_2_deg	6.044
r_mcbond_it	5.395
r_mcbond_other	5.395
r_scbond_other	4.948
r_scbond_it	4.947
r_angle_refined_deg	1.211
r_angle_other_deg	0.384
r_chiral_restr	0.048
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2186
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	21

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction