2GSN | pdb_00002gsn

Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M Bis-Tris HCl, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2	38.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.683	α = 90
b = 78.692	β = 90
c = 129.527	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	CCD	ADSC QUANTUM 210		2005-09-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.2826,1.2831,1.2782	ALS	8.2.1

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	1.75	50	98.1	0.097			67365	67365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	81.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	1.75	50	67365	63794	3398	98.21	0.17221	0.17221	0.17056	0.1823	0.2027	0.214	RANDOM	22.358

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]
-0.27			0.38		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.996
r_dihedral_angle_3_deg	12.686
r_dihedral_angle_4_deg	11.901
r_dihedral_angle_1_deg	5.938
r_scangle_it	1.833
r_scbond_it	1.265
r_angle_refined_deg	1.144
r_angle_other_deg	0.802
r_mcangle_it	0.716
r_mcbond_it	0.618
r_symmetry_vdw_other	0.286
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.2
r_nbd_other	0.189
r_nbtor_refined	0.17
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.139
r_mcbond_other	0.126
r_nbtor_other	0.081
r_chiral_restr	0.072
r_metal_ion_refined	0.042
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5882
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
BOS	data collection
SCALEPACK	data scaling
SOLVE	phasing