3C06 | pdb_00003c06

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

X-RAY DIFFRACTION

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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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.2174	0.29179	0.2873	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
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