2G08 | pdb_00002g08

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product-transition complex analog with Aluminum fluoride

X-RAY DIFFRACTION

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 20 MINUTES IN WELL SOLUTION WITH 0.060 M magnesium chloride, 0.003 M aluminum chloride, 0.050 M sodium fluoride, 0.010 M uridine, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.044	α = 90
b = 135.044	β = 90
c = 39.049	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	2005-12-18		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	2.35	67.52	99.9	0.0991	19.01	16.69		33163

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	2.35	2.4	100		0.7363	1.94	6.08	2039

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	2.35	67.52	33031	1673	99.563	0.194	0.194	0.1901	0.19	0.2603	0.26	RANDOM	43.413

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]
0.858	0.429		0.858		-1.287

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.893
r_dihedral_angle_4_deg	22.124
r_dihedral_angle_3_deg	16.836
r_dihedral_angle_1_deg	6.467
r_scangle_it	2.875
r_scbond_it	1.923
r_angle_refined_deg	1.407
r_mcangle_it	1.122
r_mcbond_it	0.701
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.893
r_dihedral_angle_4_deg	22.124
r_dihedral_angle_3_deg	16.836
r_dihedral_angle_1_deg	6.467
r_scangle_it	2.875
r_scbond_it	1.923
r_angle_refined_deg	1.407
r_mcangle_it	1.122
r_mcbond_it	0.701
r_nbtor_refined	0.304
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.18
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.104
r_metal_ion_refined	0.056
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4652
Nucleic Acid Atoms
Solvent Atoms	479
Heterogen Atoms	10

Software

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

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.