3BFI | pdb_00003bfi

E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.5 M AMMONIUM SULFATE, 20 MM REMARK 280 KH2PO4, 4 MM DTT, 4 MM 5-NO2-dUMP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.02	α = 90
b = 133.02	β = 90
c = 133.02	γ = 90

Symmetry
Space Group	I 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	DIFFRACTOMETER	ENRAF-NONIUS FAST		1997-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.2	35	93	0.081	0.081	7.5	5.1	19978	18431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.46	99

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	FOURIER SYNTHESIS	THROUGHOUT	3TMS	2.2	26.09	17489	942	92.26	0.16758	0.1651	0.17	0.21799	0.22	RANDOM	30.051

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.111
r_dihedral_angle_4_deg	22.342
r_dihedral_angle_3_deg	17.347
r_dihedral_angle_1_deg	6.421
r_scangle_it	4.217
r_scbond_it	2.656
r_mcangle_it	1.711
r_angle_refined_deg	1.657
r_mcbond_it	0.973
r_nbtor_refined	0.309
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.163
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2149
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MADNESS	data collection
PROCOR	data reduction
PROCOR	data scaling