5IOR

Flavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GT9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.6	293.15	7% PEG 4K, 100 mM NaCl, 100 mM Na/K phosphate, pH 6.6

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.679	α = 90
b = 109.679	β = 90
c = 119.864	γ = 90

Symmetry
Space Group	I 41 2 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	CCD	MARMOSAIC 300 mm CCD		2013-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03320	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	80.92	99.7	20.4	14.6		27043

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	4GT9	1.95	80.92	25671	1270	99.99	0.16341	0.16204	0.17	0.19148	0.2	RANDOM	32.196

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]
-0.99			-0.99		1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.313
r_dihedral_angle_4_deg	18.241
r_dihedral_angle_3_deg	13.055
r_dihedral_angle_1_deg	6.017
r_long_range_B_refined	5.041
r_long_range_B_other	4.986
r_scangle_other	2.844
r_scbond_it	1.747
r_mcangle_it	1.742
r_mcangle_other	1.741
r_scbond_other	1.734
r_angle_refined_deg	1.342
r_mcbond_it	1.12
r_mcbond_other	1.12
r_angle_other_deg	0.786
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	1801
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	100

Software

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