4PSG | pdb_00004psg

Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor N(4)OHdCMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	0.1M MES, 0.2M MgAcetate, 15% PEG 8000. Crystals soaked with 36mM inhibitor solution for 80min, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.412	α = 90
b = 95.893	β = 103.81
c = 82.179	γ = 90

Symmetry
Space Group	P 1 21 1

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			2014-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	Nova high-flux-micro-focus sealed tube	1.54056

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	79.804	99.8	0.237	8.1	8.7	22154	22154

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	2.8	2.95	100		0.71	0.71	1.1	8.7	3232

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.8	25.11	22128	1130	99.92	0.2333	0.2314	0.2251	0.2673	0.2594	RANDOM	16.53

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]
-0.58		-0.23	1.13		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.275
r_dihedral_angle_3_deg	23.75
r_dihedral_angle_4_deg	22.598
r_dihedral_angle_1_deg	6.732
r_angle_refined_deg	1.607
r_mcangle_it	0.71
r_mcbond_it	0.373
r_scbond_it	0.122
r_chiral_restr	0.1
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.275
r_dihedral_angle_3_deg	23.75
r_dihedral_angle_4_deg	22.598
r_dihedral_angle_1_deg	6.732
r_angle_refined_deg	1.607
r_mcangle_it	0.71
r_mcbond_it	0.373
r_scbond_it	0.122
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4632
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	42

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	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.