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Co-crystal structure of the N-termial cGMP binding domain of Plasmodium falciparum PKG with cGMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25 % Peg3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.98 37.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.266 α = 90 b = 53.847 β = 90 c = 92.351 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU SATURN A200 2015-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 1.65 50 99.7 0.043 0.046 0.017 19.4 7.4 15745
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 1.65 1.68 96.8 0.303 0.334 0.138 0.957 5.6 750
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 4MYJ 1.65 46.18 14851 813 99.22 0.1972 0.1955 0.2054 0.2268 0.2296 RANDOM 27.091
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] 0.71 0.64 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 5.985 r_mcangle_it 3.015 r_mcbond_it 2.006 r_mcbond_other 1.994 r_angle_refined_deg 1.592 r_angle_other_deg 0.951 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.808 r_dihedral_angle_4_deg 16.009 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 5.985 r_mcangle_it 3.015 r_mcbond_it 2.006 r_mcbond_other 1.994 r_angle_refined_deg 1.592 r_angle_other_deg 0.951 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1078 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing