7N1S | pdb_00007n1s

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 3350, bis-tris

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.204	α = 90
b = 77.712	β = 90
c = 129.292	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	PIXEL	DECTRIS PILATUS 6M	Rh coated collimating mirrors, K-B focusing mirrors	2018-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	66.606	100	0.101	0.109	0.041	9.7	7.3	45218	45218

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	100		1.192	1.192	1.285	0.473	0.7	7.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2GSU	2	30.61	42956	2185	99.94	0.2161	0.2139	0.2206	0.2565	0.2594	RANDOM	44.528

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]
0.06			4.2		-4.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.282
r_dihedral_angle_4_deg	16.712
r_dihedral_angle_3_deg	14.535
r_dihedral_angle_1_deg	6.627
r_angle_refined_deg	1.645
r_angle_other_deg	1.245
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5845
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction