2FTY

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% PEG 3350, 0.1M ammonium sulfate, 0.001mM zinc chloride, 0.1M bis-tris , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.428	α = 90
b = 73.32	β = 91.59
c = 162.181	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	ADSC QUANTUM 4		2004-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.931	ESRF	ID14-2

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	44.3	99.3	0.086	13.5	3.1	83629	83629			44.9

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	98.7		0.309	3.2	3	12084

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1nfg	2.4	43.85	79226	79226	4233	98.98	0.21996	0.21712	0.2737	RANDOM	35.905

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]
-0.1		0.41	2.7		-2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.512
r_dihedral_angle_4_deg	17.679
r_dihedral_angle_3_deg	15.726
r_dihedral_angle_1_deg	5.872
r_scangle_it	1.548
r_angle_refined_deg	1.193
r_scbond_it	0.983
r_mcangle_it	0.493
r_nbtor_refined	0.3
r_mcbond_it	0.296
r_symmetry_hbond_refined	0.246
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16587
Nucleic Acid Atoms
Solvent Atoms	681
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
EPMR	phasing