8UY2

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, AdoMet-bound, Inhibited (T) State

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FCX	Trimmed Catalytic domain and trimmed regulatory domain used as invidiual search models

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293.15	1-1 protein to reservoir solution, Protein: 50 mg/mL, 50 mM potassium phosphate buffer (KPB), pH 7.4, containing 500 uM AoMet and 250 uM FAD Reservoir Solution: 0.1 M sodium acetate, pH 4.8, 0.2 M ammonium sulfate, 6% polyethylene glycol monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.656	α = 90
b = 149.948	β = 90
c = 171.056	γ = 90

Symmetry
Space Group	P 2 21 21

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 9M		2022-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1271	APS	21-ID-D

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	2.83	75.087	99.8	0.126	0.149	0.077	0.987	10.1	6.9		80491

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	2.83	2.89			1.171	1.383	0.724	0.672		7.2

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.83	74.974	80381	3970	99.603	0.188	0.1873	0.2027	RANDOM	75.216

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]
-0.655			1.49		-0.835

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.794
r_lrange_other	15.554
r_lrange_it	15.551
r_dihedral_angle_3_deg	14.838
r_dihedral_angle_6_deg	13.565
r_scangle_it	9.835
r_scangle_other	9.79
r_mcangle_it	7.466
r_mcangle_other	7.465
r_dihedral_angle_1_deg	6.807
r_scbond_it	6.377
r_scbond_other	6.341
r_mcbond_it	4.894
r_mcbond_other	4.892
r_dihedral_angle_other_2_deg	1.724
r_angle_refined_deg	1.633
r_angle_other_deg	1.37
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.187
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.141
r_nbd_other	0.117
r_xyhbond_nbd_refined	0.108
r_ncsr_local_group_6	0.101
r_chiral_restr	0.094
r_ncsr_local_group_3	0.094
r_ncsr_local_group_1	0.093
r_ncsr_local_group_4	0.093
r_symmetry_xyhbond_nbd_refined	0.092
r_ncsr_local_group_5	0.092
r_ncsr_local_group_2	0.091
r_symmetry_nbtor_other	0.065
r_gen_planes_refined	0.011
r_bond_other_d	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17822
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	502

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing