2G06 | pdb_00002g06

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with bound magnesium(II)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 15 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, temperature 277K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.343	α = 90
b = 134.343	β = 90
c = 39.152	γ = 120

Symmetry
Space Group	P 32

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	BRUKER PROTEUM-R	MONTEL OPTICS	2006-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	67.17	100	0.1006	20.61	17.82		37523

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	2.3	100		0.6371	2.67	6.47	2423

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 (All)	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 entry 2BDU	2.25	67.17	37505	1899	99.955	0.158	0.158	0.1548	0.16	0.2193	0.22	RANDOM	35.072

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]
0.204	0.102		0.204		-0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.774
r_dihedral_angle_4_deg	22.555
r_dihedral_angle_3_deg	15.516
r_scangle_it	5.969
r_dihedral_angle_1_deg	5.893
r_scbond_it	4.389
r_mcangle_it	2.236
r_angle_refined_deg	1.474
r_mcbond_it	1.291
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.249
r_xyhbond_nbd_refined	0.212
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.193
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4652
Nucleic Acid Atoms
Solvent Atoms	815
Heterogen Atoms	38

Software

Software
Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing