6LL7

Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mn-activated 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	6	293	30%(w/v) PEG3350, 0.5 M NaCl, 0.1 M glycine and 0.1 M citrate

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.53	α = 107.397
b = 75.57	β = 90.06
c = 85.67	γ = 92.169

Symmetry
Space Group	P 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	2018-10-17	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	2.2	48	96.8	0.123	0.146	0.992	6.88	3.494		61908			37.615

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	2.2	2.33	95.4		0.637	0.747	0.764	1.98	3.665

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HAW	2.2	47.509	60604	2985	94.973	0.258	0.2561	0.2972	39.534

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]
-1.314	1.854	-0.157	3.041	0.448	-1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.751
r_dihedral_angle_4_deg	16.04
r_dihedral_angle_3_deg	14.76
r_dihedral_angle_1_deg	7.124
r_lrange_it	3.045
r_lrange_other	3.025
r_mcangle_it	1.631
r_mcangle_other	1.631
r_scangle_it	1.516
r_scangle_other	1.516
r_angle_refined_deg	1.4
r_angle_other_deg	1.208
r_mcbond_it	0.97
r_mcbond_other	0.97
r_scbond_it	0.894
r_scbond_other	0.89
r_symmetry_nbd_refined	0.341
r_nbd_refined	0.189
r_nbd_other	0.185
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.128
r_symmetry_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.075
r_xyhbond_nbd_other	0.075
r_chiral_restr	0.06
r_ncsr_local_group_1	0.039
r_ncsr_local_group_4	0.039
r_ncsr_local_group_2	0.038
r_ncsr_local_group_5	0.037
r_ncsr_local_group_6	0.033
r_ncsr_local_group_3	0.027
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_ext_dist_refined_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9360
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	10

Software

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