2GSO | pdb_00002gso

Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1M Bis-Tris HCl, 18% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.04	α = 90
b = 78.776	β = 90
c = 129.686	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 315		2005-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537	ALS	8.2.2

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	1.3	50	89.4	0.085			147720	147720

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.35	28.3

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	FOURIER SYNTHESIS	THROUGHOUT	1.3	50	147720	140234	7390	89.25	0.17304	0.17304	0.17201	0.1816	0.19313	0.2034	RANDOM	14.567

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]
0.05			0.01		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.122
r_dihedral_angle_4_deg	12.511
r_dihedral_angle_3_deg	12.193
r_sphericity_bonded	7.216
r_dihedral_angle_1_deg	5.944
r_rigid_bond_restr	2.874
r_scangle_it	2.177
r_sphericity_free	1.869
r_scbond_it	1.463
r_angle_refined_deg	1.235
r_mcangle_it	0.901
r_angle_other_deg	0.806
r_mcbond_it	0.784
r_symmetry_vdw_other	0.254
r_nbd_refined	0.203
r_nbd_other	0.188
r_nbtor_refined	0.174
r_mcbond_other	0.158
r_symmetry_vdw_refined	0.146
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.11
r_nbtor_other	0.081
r_chiral_restr	0.074
r_metal_ion_refined	0.035
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6038
Nucleic Acid Atoms
Solvent Atoms	847
Heterogen Atoms	14

Software

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