1GTH | pdb_00001gth

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 5 MM 5-IODOURACIL, 5 MM NADPH

Crystal Properties
Matthews coefficient	Solvent content
2.46	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.21	α = 90
b = 159.69	β = 97.11
c = 167.59	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		2000-10-09	M	SINGLE WAVELENGTH

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

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	2.25	30	98.3	0.064	14.3	3.6		200114			27.5

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	2.25	2.37	97.4		0.25	5.2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED	2.25	25	199143	3984	98.1	0.177	0.177	0.1747	0.209	0.2048	RANDOM	33.3

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]
-8.16		0.91	9.51		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.9
c_improper_angle_d	3.11
c_angle_deg	1.4
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30999
Nucleic Acid Atoms
Solvent Atoms	3073
Heterogen Atoms	690

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing