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Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium Vivax - AMPPNP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 18.2% PEG3350, 0.1 M HEPES pH 7.0, 0.1M Succinate, 2mM MgCl2,5mM AMPPNP
Crystal Properties Matthews coefficient Solvent content 3.97 69.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.111 α = 90 b = 117.906 β = 95.08 c = 67.731 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 2015-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 99.1 0.09 0.104 0.05 7 4.1 65835
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 95.5 0.845 0.973 0.475 0.698 3.7 6286
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4MYI 2.3 50 62646 3186 98.42 0.2228 0.2212 0.255 0.2415 RANDOM 74.39
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] 1.85 0.15 -4.14 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_4_deg 14.494 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_1_deg 5.906 r_mcangle_it 1.487 r_angle_refined_deg 1.361 r_angle_other_deg 0.917 r_mcbond_it 0.811 r_mcbond_other 0.811 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.736 r_dihedral_angle_4_deg 14.494 r_dihedral_angle_3_deg 13.706 r_dihedral_angle_1_deg 5.906 r_mcangle_it 1.487 r_angle_refined_deg 1.361 r_angle_other_deg 0.917 r_mcbond_it 0.811 r_mcbond_other 0.811 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6395 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 42
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing