3BZ0 | pdb_00003bz0

Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00

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	1mM EDTA, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.916	α = 90
b = 77.916	β = 90
c = 224.183	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	MARMOSAIC 225 mm CCD		2005-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	1.078	EMBL/DESY, HAMBURG	BW7B

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	2.7	33.37	88.6	0.139	0.139	4.3	4	10447	10443		1.7	56.53

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	2.7	2.85	92.3		0.439	0.439	1.7	4.1	1502

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	2.7	33.37	10443	9511	932	88.6	0.2349	0.22582	0.23	0.32619	0.32	RANDOM	37.422

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]
0.02	0.01		0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.425
r_dihedral_angle_3_deg	24.324
r_dihedral_angle_4_deg	23.758
r_dihedral_angle_1_deg	8.06
r_scangle_it	2.955
r_angle_refined_deg	2.151
r_scbond_it	1.933
r_mcangle_it	1.518
r_mcbond_it	0.86
r_nbtor_refined	0.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.425
r_dihedral_angle_3_deg	24.324
r_dihedral_angle_4_deg	23.758
r_dihedral_angle_1_deg	8.06
r_scangle_it	2.955
r_angle_refined_deg	2.151
r_scbond_it	1.933
r_mcangle_it	1.518
r_mcbond_it	0.86
r_nbtor_refined	0.331
r_symmetry_vdw_refined	0.329
r_nbd_refined	0.284
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.154
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2521
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	45

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.