2G07 | pdb_00002g07

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium 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 beryllium fluoride, 0.050 M sodium fluoride, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.834	α = 90
b = 134.834	β = 90
c = 38.945	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	2006-01-20		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	2.3	67.42	93.9	0.1278	11.32	7.7		33047

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	2.3	2.35	83.8		0.6356	1.99	4.11	1805

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	2.3	67.42	33027	1673	93.901	0.184	0.184	0.1799	0.18	0.2585	0.26	RANDOM	38.491

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]
-0.155	-0.078		-0.155		0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.608
r_dihedral_angle_4_deg	19.773
r_dihedral_angle_3_deg	16.423
r_dihedral_angle_1_deg	6.504
r_scangle_it	3.063
r_scbond_it	2.127
r_angle_refined_deg	1.664
r_mcangle_it	1.219
r_mcbond_it	0.84
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.608
r_dihedral_angle_4_deg	19.773
r_dihedral_angle_3_deg	16.423
r_dihedral_angle_1_deg	6.504
r_scangle_it	3.063
r_scbond_it	2.127
r_angle_refined_deg	1.664
r_mcangle_it	1.219
r_mcbond_it	0.84
r_nbtor_refined	0.305
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.174
r_chiral_restr	0.119
r_metal_ion_refined	0.051
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4660
Nucleic Acid Atoms
Solvent Atoms	538
Heterogen Atoms	2

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.