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Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mn-activated 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 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
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HAW 2.2 47.509 60604 2985 94.973 0.258 0.2561 0.2587 0.2972 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
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