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Crystal structure of PfPK7 in complex with an ATP-site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PML PfPK7 in complex with 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% PEG10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.406 α = 90 b = 82.084 β = 90 c = 138.962 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 2006-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 2.75 20 97.7 0.066 15.8 3.7 10971 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 2.8 2.871 87.3 0.461 2.1
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 ATP analogue (2PML) 2.8 20 2 10971 9946 499 98.22 0.22277 0.2192 0.2125 0.29559 0.2899 RANDOM 38.814
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] 3.27 -0.57 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_3_deg 19.621 r_dihedral_angle_4_deg 18.543 r_dihedral_angle_1_deg 6.81 r_angle_refined_deg 1.309 r_scangle_it 1.24 r_mcangle_it 0.839 r_scbond_it 0.762 r_mcbond_it 0.463 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_3_deg 19.621 r_dihedral_angle_4_deg 18.543 r_dihedral_angle_1_deg 6.81 r_angle_refined_deg 1.309 r_scangle_it 1.24 r_mcangle_it 0.839 r_scbond_it 0.762 r_mcbond_it 0.463 r_nbtor_refined 0.317 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2856 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing