8DAE | pdb_00008dae

Arabidopsis thaliana bifunctional dihydrofolate reductase-thymidylate synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I3R	PDB entry 3I3R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 35% w/v poly(acrylic acid sodium salt)2100

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.717	α = 90
b = 80.717	β = 90
c = 181.757	γ = 90

Symmetry
Space Group	P 42 21 2

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 16M		2020-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2	48.381	100	1	18.2	26.3		41582

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	2	2.05			0.37

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 3I3R	2	48.381	41519	2072	99.952	0.204	0.2021	0.21	0.2373	0.24	51.554

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]
-0.713			-0.713		1.426

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.531
r_dihedral_angle_4_deg	18.004
r_dihedral_angle_3_deg	15.809
r_lrange_it	8.587
r_lrange_other	8.586
r_dihedral_angle_1_deg	7.184
r_scangle_it	6.79
r_scangle_other	6.79
r_mcangle_it	5.947
r_mcangle_other	5.946
r_scbond_it	4.642
r_scbond_other	4.641
r_mcbond_it	4.313
r_mcbond_other	4.313
r_angle_refined_deg	1.502
r_angle_other_deg	1.363
r_nbd_other	0.238
r_symmetry_nbd_refined	0.216
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3651
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms

Software

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