3EAW | pdb_00003eaw

Replacement of Val3 in Human Thymidylate Synthase Affects Its Kinetic Properties and Intracellular Stability

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	20-25%ammonium sulfate, 20mM BME, 0.1M Tris PH8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.704	α = 90
b = 95.704	β = 90
c = 81.94	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 300 mm CCD		2008-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM		APS	22-BM

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	1.86	50	91.6	0.061	35.545	5.1		33751

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)
	1.86	1.93	57.5		0.392		2.1	2093

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.86	50	33719	1691	91.62	0.232	0.23	0.22	0.268	RANDOM	47.43

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]
-1.4	-0.7		-1.4		2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.017
r_dihedral_angle_3_deg	18.75
r_dihedral_angle_4_deg	18.119
r_dihedral_angle_1_deg	6.955
r_scangle_it	4.834
r_scbond_it	3.228
r_mcangle_it	2.369
r_angle_refined_deg	2.01
r_mcbond_it	1.443
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.017
r_dihedral_angle_3_deg	18.75
r_dihedral_angle_4_deg	18.119
r_dihedral_angle_1_deg	6.955
r_scangle_it	4.834
r_scbond_it	3.228
r_mcangle_it	2.369
r_angle_refined_deg	2.01
r_mcbond_it	1.443
r_nbtor_refined	0.319
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.191
r_chiral_restr	0.153
r_symmetry_hbond_refined	0.096
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2101
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.