6LL8

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HAW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.428524%(w/v) PEG3350, 10 mM ammonium phosphate dibasic and 0.2 M NaCl., 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.49α = 90
b = 78.98β = 98.593
c = 75.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors2019-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.346.696.60.0450.0510.99918.214.64414917817.793
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)RedundancyNumber Unique Reflections (All)
11.31.3472.30.30.3660.9063.052.617

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HAW1.346.568149178754098.2710.0980.09650.121614.123
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]
0.4690.148-0.022-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.083
r_dihedral_angle_4_deg14.566
r_dihedral_angle_3_deg11.608
r_dihedral_angle_1_deg6.599
r_lrange_it2.925
r_lrange_other2.691
r_scangle_it2.37
r_scangle_other2.37
r_rigid_bond_restr2.249
r_scbond_it1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.083
r_dihedral_angle_4_deg14.566
r_dihedral_angle_3_deg11.608
r_dihedral_angle_1_deg6.599
r_lrange_it2.925
r_lrange_other2.691
r_scangle_it2.37
r_scangle_other2.37
r_rigid_bond_restr2.249
r_scbond_it1.98
r_scbond_other1.98
r_angle_refined_deg1.796
r_angle_other_deg1.562
r_mcangle_other1.307
r_mcangle_it1.305
r_mcbond_it1.023
r_mcbond_other1.014
r_nbd_refined0.23
r_symmetry_nbd_other0.179
r_symmetry_xyhbond_nbd_refined0.177
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.163
r_nbd_other0.162
r_symmetry_nbd_refined0.143
r_chiral_restr0.108
r_symmetry_nbtor_other0.086
r_symmetry_xyhbond_nbd_other0.047
r_metal_ion_refined0.015
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4680
Nucleic Acid Atoms
Solvent Atoms971
Heterogen Atoms85

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
XDSdata reduction