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Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (R3 crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 1.6% Tacsimate pH 5.0, 80 mM Na Citrate tribasic pH 5.6, 12.8% PEG 3350, 20% Glycerol
Bromelain 5 ug/ml
MtPPA1 7.7 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.784 α = 90 b = 81.784 β = 90 c = 176.935 γ = 120
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 PILATUS3 6M 2017-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 1.84 50 99.2 0.045 0.049 1 17.22 5.6 37764
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 1.84 1.95 95.7 0.87 0.96 0.79 1.7 5.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4lug 1.84 40.89 36742 1020 99.17 0.16547 0.16449 0.1725 0.20108 0.2073 RANDOM 50.482
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] 0.77 0.39 0.77 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 14.494 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 7.232 r_long_range_B_refined 6.669 r_long_range_B_other 6.651 r_scangle_other 4.528 r_mcangle_it 3.207 r_mcangle_other 3.206 r_scbond_it 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 14.494 r_dihedral_angle_3_deg 13.584 r_dihedral_angle_1_deg 7.232 r_long_range_B_refined 6.669 r_long_range_B_other 6.651 r_scangle_other 4.528 r_mcangle_it 3.207 r_mcangle_other 3.206 r_scbond_it 2.927 r_scbond_other 2.926 r_mcbond_it 2.187 r_mcbond_other 2.186 r_angle_refined_deg 1.519 r_angle_other_deg 0.964 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing XDS data scaling