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Crystal structure of Inorganic Pyrophosphatase from Medicago truncatula (I23 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, SITTING DROP 6 292 4% Tacsimate pH 6.0, 12% PEG 3350
crystal after 3 months
20% Ethylene glycol as cryoprotectant
MtPPA1 at 16.3 mg/ml
Crystal Properties Matthews coefficient Solvent content 5.5 81.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 235.202 α = 90 b = 235.202 β = 90 c = 235.202 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-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 2.89 50 99.7 0.14 0.14 1 23.4 16 48141
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 2.89 3.07 98.2 1.7 1.8 0.65 1.9 15
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 2.89 48.01 47082 1060 99.67 0.17278 0.17227 0.1787 0.19529 0.1967 RANDOM 83.382
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.748 r_dihedral_angle_3_deg 17.796 r_dihedral_angle_4_deg 16.887 r_long_range_B_refined 7.371 r_long_range_B_other 7.37 r_dihedral_angle_1_deg 6.728 r_scangle_other 4.989 r_mcangle_it 4.475 r_mcangle_other 4.475 r_scbond_it 2.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.748 r_dihedral_angle_3_deg 17.796 r_dihedral_angle_4_deg 16.887 r_long_range_B_refined 7.371 r_long_range_B_other 7.37 r_dihedral_angle_1_deg 6.728 r_scangle_other 4.989 r_mcangle_it 4.475 r_mcangle_other 4.475 r_scbond_it 2.941 r_scbond_other 2.941 r_mcbond_it 2.622 r_mcbond_other 2.621 r_angle_refined_deg 1.46 r_angle_other_deg 0.944 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 5737 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing XDS data scaling