4EZ8 | pdb_00004ez8

Crystal structure of mouse thymidylate sythase in ternary complex with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate and the cofactor product, dihydrofolate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		280	MES, PEG 8K, MgAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.121	α = 90
b = 112.045	β = 90
c = 88.297	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2011-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

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	1.17	50	99	0.084	9.8	5.4	118524	117370		-3

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	1.17	1.19	91.7		0.488		3	5388

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.17	21.35	118524	117324	5872	99.04	0.1084	0.1072	0.11	0.1295	0.13	RANDOM	15.1112

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.057
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_3_deg	12.12
r_scangle_it	6.785
r_dihedral_angle_1_deg	6.294
r_scbond_it	4.888
r_mcangle_it	3.388
r_mcbond_it	2.341
r_rigid_bond_restr	2.114
r_angle_refined_deg	2.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.057
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_3_deg	12.12
r_scangle_it	6.785
r_dihedral_angle_1_deg	6.294
r_scbond_it	4.888
r_mcangle_it	3.388
r_mcbond_it	2.341
r_rigid_bond_restr	2.114
r_angle_refined_deg	2.013
r_angle_other_deg	1.032
r_mcbond_other	0.794
r_chiral_restr	0.132
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2319
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	65

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

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.