8EAC

Thermus thermophilus methylenetetrahydrofolate reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3APT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	297	0.1M Hepes pH7.8, 1M LiCl, 20% PEG6k

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.284	α = 90
b = 89.055	β = 90
c = 161.207	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		2021-07-02	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)	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	1.9	89.06	97.7	0.996	12.7	6.5		49988

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.965

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3apt	1.9	80.734	49922	2534	97.354	0.209	0.2065	0.2501	30.143

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]
2.602			-0.995		-1.608

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.09
r_dihedral_angle_4_deg	20.208
r_dihedral_angle_3_deg	15.624
r_lrange_it	7.362
r_lrange_other	7.353
r_dihedral_angle_1_deg	6.31
r_scangle_it	5.374
r_scangle_other	5.373
r_mcangle_it	3.939
r_mcangle_other	3.939
r_scbond_it	3.462
r_scbond_other	3.461
r_mcbond_other	2.669
r_mcbond_it	2.668
r_angle_refined_deg	1.594
r_angle_other_deg	1.318
r_symmetry_xyhbond_nbd_refined	0.339
r_symmetry_nbd_refined	0.285
r_nbd_refined	0.213
r_nbd_other	0.213
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4489
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	53

Software

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