2NXF | pdb_00002nxf

Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (10.4% PEG 4K, 0.40 M sodium chloride, 0.10 M HEPES pH 7.5) Cryoprotected with: 15% PEG 8K, 0.30 M ammonium thiocyanate, 0.010 M sodium dihydrogen phosphate, 0.0005 M zinc sulfate, 0.10 M HEPPS pH 8.5 supplemented with up to 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.584	α = 90
b = 86.593	β = 90
c = 157.315	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-11-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97923, 0.96400	APS	23-ID-D

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	1.7	48.276	99.8	0.083	14.348	13.6		47311

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	1.7	1.74	98.1		0.431	3.077	8.2	3077

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.7	48.276	47258	2369	99.728	0.162	0.161	0.169	0.18	0.1875	RANDOM	27.996

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]
0.338			0.711		-1.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.837
r_dihedral_angle_4_deg	17.009
r_dihedral_angle_3_deg	11.915
r_dihedral_angle_1_deg	5.089
r_scangle_it	3.138
r_scbond_it	2.026
r_angle_refined_deg	1.241
r_mcangle_it	1.156
r_mcbond_it	0.71
r_nbtor_refined	0.303
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.092
r_metal_ion_refined	0.028
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2524
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction