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Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mg-PNP form
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 0.0968 0.1216 0.1215 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
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