6LL8 | pdb_00006ll8

Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	285	24%(w/v) PEG3350, 10 mM ammonium phosphate dibasic and 0.2 M NaCl., 0.1 M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.49	α = 90
b = 78.98	β = 98.593
c = 75.3	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER X 16M	mirrors	2019-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	46.6	96.6	0.045	0.051	0.999	18.21	4.644		149178			17.793

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.34	72.3		0.3	0.366	0.906	3.05	2.617

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HAW	1.3	46.568	149178	7540	98.271	0.098	0.0965	0.1	0.1216	0.12	14.123

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]
0.469		0.148	-0.022		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.083
r_dihedral_angle_4_deg	14.566
r_dihedral_angle_3_deg	11.608
r_dihedral_angle_1_deg	6.599
r_lrange_it	2.925
r_lrange_other	2.691
r_scangle_it	2.37
r_scangle_other	2.37
r_rigid_bond_restr	2.249
r_scbond_it	1.98
r_scbond_other	1.98
r_angle_refined_deg	1.796
r_angle_other_deg	1.562
r_mcangle_other	1.307
r_mcangle_it	1.305
r_mcbond_it	1.023
r_mcbond_other	1.014
r_nbd_refined	0.23
r_symmetry_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.162
r_symmetry_nbd_refined	0.143
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.047
r_metal_ion_refined	0.015
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4680
Nucleic Acid Atoms
Solvent Atoms	971
Heterogen Atoms	85

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
XDS	data reduction