3IK1 | pdb_00003ik1

Lactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 20C

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TDM	PDB ENTRY 2TDM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.985	α = 90
b = 77.985	β = 90
c = 224.718	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 315r		2008-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.983	ESRF	ID23-1

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	2.25	74.95	99.9	0.079	0.079	37.7	19.9		20159	1	2	33.669

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	2.25	2.37	100		0.286	0.286	10.8	20.9	2868

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 2TDM	2.25	67.54	2	20103	19048	1024	99.85	0.21457	0.21164	0.2	0.27083	0.26	RANDOM	37.159

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.501
r_dihedral_angle_4_deg	22.565
r_dihedral_angle_3_deg	18.809
r_dihedral_angle_1_deg	6.677
r_scangle_it	4.36
r_scbond_it	2.858
r_mcangle_it	2.076
r_angle_refined_deg	2.027
r_mcbond_it	1.123
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.501
r_dihedral_angle_4_deg	22.565
r_dihedral_angle_3_deg	18.809
r_dihedral_angle_1_deg	6.677
r_scangle_it	4.36
r_scbond_it	2.858
r_mcangle_it	2.076
r_angle_refined_deg	2.027
r_mcbond_it	1.123
r_chiral_restr	0.136
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2561
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	42

Software

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

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.