3BHL | pdb_00003bhl

E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TSC	pdb entry 2TSC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.5 M ammonium sulfate, 20 mm KH2PO4, 4mm DTT, 4 mM 5-NO2dump, 4MM methylenetetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.87	α = 90
b = 124.87	β = 90
c = 66.394	γ = 120

Symmetry
Space Group	P 63

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	ADSC QUANTUM 4		2002-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9	APS	14-BM-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.4	105.41	100	0.076	18.6	6.4	115632	115632

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	100		0.45	3.2	6.3

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	pdb entry 2TSC	1.4	25	109776	5799	99.74	0.17564	0.1742	0.18	0.20299	0.21	RANDOM	10.792

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.845
r_dihedral_angle_4_deg	23.521
r_dihedral_angle_3_deg	13.556
r_dihedral_angle_1_deg	6.453
r_scangle_it	3.394
r_scbond_it	2.271
r_angle_other_deg	1.984
r_angle_refined_deg	1.786
r_mcangle_it	1.511
r_mcbond_it	0.854
r_chiral_restr	0.302
r_symmetry_vdw_other	0.302
r_mcbond_other	0.249
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.132
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
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_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4306
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	125

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling