3C06

Lactobacillus CASEI Thymidylate Synthase Ternary Complex With DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl, 100mM ammonium phosphate, 5% PEG 400 (v/v), 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.573	α = 90
b = 76.573	β = 90
c = 212.931	γ = 120

Symmetry
Space Group	P 61 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	ADSC QUANTUM 4		2005-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.930	ESRF	ID14-1

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	2.6	38.29	98.6	0.1	0.1	6.4	8.4	11884	11884		1.7	57.048

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	99.6		0.434	0.434	1.7	9	1700

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LCA	2.6	38.29	11884	11312	565	100	0.22212	0.21864	0.29179	RANDOM	40.999

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]
0.11	0.05		0.11		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.782
r_dihedral_angle_4_deg	24.888
r_dihedral_angle_3_deg	23.765
r_dihedral_angle_1_deg	7.953
r_scangle_it	2.903
r_angle_refined_deg	2.115
r_scbond_it	1.994
r_mcangle_it	1.543
r_mcbond_it	0.856
r_nbtor_refined	0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.782
r_dihedral_angle_4_deg	24.888
r_dihedral_angle_3_deg	23.765
r_dihedral_angle_1_deg	7.953
r_scangle_it	2.903
r_angle_refined_deg	2.115
r_scbond_it	1.994
r_mcangle_it	1.543
r_mcbond_it	0.856
r_nbtor_refined	0.327
r_symmetry_hbond_refined	0.262
r_nbd_refined	0.258
r_symmetry_vdw_refined	0.246
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.126
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2487
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.