3NUQ | pdb_00003nuq

Structure of a putative nucleotide phosphatase from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Cr dataset at wavelength of 2.27 A, with a Rigaku MicroMax-007 HF generator and a Cr Raxis4++ detector. This was subsequently refined using a Cu-wavelength dataset deposited here.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	0.1M Bis-Tris pH6.5, 25 PEG 2K MME (monomethyl ether) cryoprotected with 25% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.474	α = 90
b = 64.664	β = 90
c = 67.708	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	RIGAKU RAXIS HTC	mirrors	2008-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.54178

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	1.6	23.38	95.5	0.077	0.077	14.95	5.7	34511		-3

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)
	1.6	1.66	97.4		0.347	2.7	1.9

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	SAD	THROUGHOUT	Cr dataset at wavelength of 2.27 A, with a Rigaku MicroMax-007 HF generator and a Cr Raxis4++ detector. This was subsequently refined using a Cu-wavelength dataset deposited here.	1.7	23.38	25924	2889	99.78	0.19722	0.19395	0.19	0.22611	0.22	RANDOM	17.81

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.939
r_dihedral_angle_4_deg	18.791
r_dihedral_angle_3_deg	13.916
r_dihedral_angle_1_deg	5.781
r_scangle_it	3.952
r_scbond_it	2.408
r_mcangle_it	1.427
r_angle_refined_deg	1.405
r_mcbond_it	0.773
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.258
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.192
r_metal_ion_refined	0.168
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2152
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	18

Software

Software
Software Name	Purpose
CrystalClear	data collection
SHELXCD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling