8UY1

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A175W7M4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	1-1 ratio protein to reservoir solution Protein: 25 mM Tris, pH 7.4, 50 mM potassium chloride, 500 uM FAD, and 1 mM TCEP Reservoir Solution: 0.1 M HEPES, pH 7.5, 0.1 mM potassium chloride, 20 mM magnesium chloride, 22% poly(acrylic acid sodium salt) 5,100

Crystal Properties
Matthews coefficient	Solvent content
3	58.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.972	α = 90
b = 151.38	β = 90
c = 188.048	γ = 90

Symmetry
Space Group	P 21 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		2022-06-30	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	3.41	52.04	99.5	0.164	0.177	0.067	0.996	7.7	6.9		46407

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	3.41	3.53		99.7	2.805	3.024	1.122	0.466		7.1

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	3.49	52.04	41089	2181	99.41	0.21759	0.21556	0.25564	RANDOM	157.458

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]
7.35			-3.86		-3.49

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	17.568
r_long_range_B_other	17.568
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_2_deg	11.609
r_mcangle_it	10.921
r_mcangle_other	10.921
r_scangle_other	10.875
r_dihedral_angle_1_deg	7.286
r_mcbond_it	6.929
r_mcbond_other	6.929
r_scbond_it	6.706
r_scbond_other	6.705
r_angle_refined_deg	1.839
r_angle_other_deg	1.382
r_chiral_restr	0.101
r_gen_planes_refined	0.014
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_bond_other_d	0.008
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	19085
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	212

Software

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