3Q91 | pdb_00003q91

Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosphatase (NUDT14)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G0S	PDB entries 1G0S, 1VIQ, 1VIU and 2DSB
experimental model	PDB	1VIQ	PDB entries 1G0S, 1VIQ, 1VIU and 2DSB
experimental model	PDB	1VIU	PDB entries 1G0S, 1VIQ, 1VIU and 2DSB
experimental model	PDB	2DSB	PDB entries 1G0S, 1VIQ, 1VIU and 2DSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	20 % w/v PEG3350, 0.2 M AMMONIUM FORMATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.04	α = 90
b = 106.24	β = 90
c = 106.35	γ = 90

Symmetry
Space Group	P 2 21 21

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	RAYONIX MX-225	MIRRORS	2009-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	53.17	99.7	0.063	0.063	8.5	4.8	26804	26724		-3	83.8

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)
	2.7	2.85	99.5		0.708	0.708	2.1	4.8	3827

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	PDB entries 1G0S, 1VIQ, 1VIU and 2DSB	2.7	53.17	25328	1376	99.53	0.23054	0.22844	0.22	0.27137	0.26	RANDOM	68.955

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]
4.87			-2.13		-2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.676
r_dihedral_angle_3_deg	15.718
r_dihedral_angle_4_deg	12.61
r_dihedral_angle_1_deg	6.158
r_scangle_it	1.438
r_angle_refined_deg	1.068
r_scbond_it	0.84
r_angle_other_deg	0.767
r_mcangle_it	0.628
r_mcbond_it	0.322
r_chiral_restr	0.061
r_mcbond_other	0.048
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4399
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling