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Crystal structure of PfPK7 in complex with hymenialdisine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PML PfPK7 in complex with an ATP analogue (2PML)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 0.1 M Hepes pH7.5; 20% PEG 10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.061 α = 90 b = 82.473 β = 90 c = 138.717 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 ADSC QUANTUM 4 2005-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3
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 2.9 69.34 99.7 0.096 11 3.6 9580 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.975 100 0.478 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PfPK7 in complex with an ATP analogue (2PML) 2.9 69.34 2 9580 9098 460 99.5 0.23453 0.23044 0.2243 0.3158 0.312 RANDOM 36.177
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] 3.82 -1.77 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_3_deg 19.846 r_dihedral_angle_4_deg 14.83 r_dihedral_angle_1_deg 6.018 r_angle_refined_deg 1.375 r_scangle_it 0.842 r_mcangle_it 0.581 r_scbond_it 0.574 r_mcbond_it 0.327 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.002 r_dihedral_angle_3_deg 19.846 r_dihedral_angle_4_deg 14.83 r_dihedral_angle_1_deg 6.018 r_angle_refined_deg 1.375 r_scangle_it 0.842 r_mcangle_it 0.581 r_scbond_it 0.574 r_mcbond_it 0.327 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2856 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing