2FVK

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FTY	PDB entry 2fty

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% PEG 3350, 0.1M ammonium sulfate, 1mM CaCl2, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.13	α = 90
b = 71.6	β = 91.4
c = 161.89	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	MARRESEARCH		2005-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	2.4	54.23	99.2	0.097	11	2.9	80380	80380			43.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	95.7		0.329	2.3	2.6	11234

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2fty	2.4	54.23	80363	80363	4085	99.14	0.18064	0.17784	0.23352	RANDOM	34.204

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]
-0.9		-1.87	2.76		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.861
r_dihedral_angle_4_deg	17.567
r_dihedral_angle_3_deg	15.297
r_dihedral_angle_1_deg	5.885
r_scangle_it	1.508
r_angle_refined_deg	1.179
r_scbond_it	1.013
r_mcangle_it	0.458
r_nbtor_refined	0.301
r_mcbond_it	0.257

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.861
r_dihedral_angle_4_deg	17.567
r_dihedral_angle_3_deg	15.297
r_dihedral_angle_1_deg	5.885
r_scangle_it	1.508
r_angle_refined_deg	1.179
r_scbond_it	1.013
r_mcangle_it	0.458
r_nbtor_refined	0.301
r_mcbond_it	0.257
r_symmetry_vdw_refined	0.238
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16594
Nucleic Acid Atoms
Solvent Atoms	1043
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	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.