5TC4 | pdb_00005tc4

Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Phosphate/Citrate pH 4.1, 38 % v/v PEG300, in presence of 1:50 ratio each of trypsin, alpha-chymotrypsin, pepsin, papain, proteinase K and subtilisin to MTHFD2

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.323	α = 90
b = 74.323	β = 90
c = 98.62	γ = 90

Symmetry
Space Group	I 4

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 PILATUS 2M		2015-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.89	37.16	99.8	0.316	0.98	6.8	6.9		21322

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.93	96.8		4.348	0.297	0.9	6.7

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 (Observed)	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	1B0A	1.89	37.16	20245	1073	99.76	0.16509	0.1626	0.17	0.21222	0.22	RANDOM	28.27

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.827
r_dihedral_angle_4_deg	20.267
r_dihedral_angle_3_deg	15.236
r_long_range_B_refined	6.253
r_long_range_B_other	6.066
r_dihedral_angle_1_deg	6.042
r_scangle_other	2.602
r_angle_refined_deg	2.276
r_scbond_it	1.642
r_scbond_other	1.64
r_mcangle_other	1.431
r_mcangle_it	1.43
r_angle_other_deg	1.17
r_mcbond_it	0.901
r_mcbond_other	0.897
r_chiral_restr	0.137
r_bond_refined_d	0.023
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	2216
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	83

Software

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