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Crystal structure of PPK2 class III in complex with Guanosine 5-tetraphosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.1 M Ammonium tartrate dibasic
Crystal Properties Matthews coefficient Solvent content 3.92 68.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.812 α = 90 b = 110.812 β = 90 c = 178.807 γ = 90
Symmetry Space Group I 41 2 2
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 ADSC QUANTUM 315r 2013-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 36.2 99.8 0.08 25 7.5 17542
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.65 36.17 15516 825 98.78 0.19616 0.19398 0.2026 0.23813 0.2518 RANDOM 65
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.012 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_3_deg 17.929 r_long_range_B_other 13.011 r_long_range_B_refined 13.01 r_scangle_other 10.004 r_mcangle_it 8.826 r_mcangle_other 8.826 r_scbond_other 6.797 r_scbond_it 6.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.012 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_3_deg 17.929 r_long_range_B_other 13.011 r_long_range_B_refined 13.01 r_scangle_other 10.004 r_mcangle_it 8.826 r_mcangle_other 8.826 r_scbond_other 6.797 r_scbond_it 6.792 r_mcbond_it 6.319 r_mcbond_other 6.301 r_dihedral_angle_1_deg 5.975 r_angle_refined_deg 1.493 r_angle_other_deg 1.095 r_chiral_restr 0.163 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2357 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing