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P. falciparum FIKK13 in complex with ATPgammaS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.2 M LiCl, 20% w/v PEG 6,000, 10% v/v Ethylene Glycol, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 1.71 27.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.397 α = 90 b = 121.657 β = 90.02 c = 151.059 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) R Split (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 2.81 64.17 99.8 0.196 0.079 0.995 0.212 6.8 7 72257 55.6
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 2.81 2.86 96.1 2.123 2.286 0.844 0.614 0.4 7.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.814 64.169 72156 3699 99.686 0.245 0.2423 0.2423 0.2862 0.2861 74.501
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] -0.124 -0.015 -0.963 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.05 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_6_deg 14.689 r_lrange_it 7.863 r_dihedral_angle_1_deg 6.796 r_scangle_it 4.189 r_mcangle_it 3.694 r_scbond_it 2.632 r_mcbond_it 2.219 r_angle_refined_deg 1.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.05 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_6_deg 14.689 r_lrange_it 7.863 r_dihedral_angle_1_deg 6.796 r_scangle_it 4.189 r_mcangle_it 3.694 r_scbond_it 2.632 r_mcbond_it 2.219 r_angle_refined_deg 1.549 r_symmetry_nbd_refined 0.32 r_nbtor_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.238 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_13 0.132 r_ncsr_local_group_18 0.123 r_ncsr_local_group_8 0.121 r_ncsr_local_group_11 0.119 r_ncsr_local_group_6 0.116 r_ncsr_local_group_14 0.115 r_ncsr_local_group_17 0.109 r_ncsr_local_group_9 0.106 r_chiral_restr 0.099 r_ncsr_local_group_12 0.091 r_ncsr_local_group_10 0.084 r_ncsr_local_group_4 0.082 r_ncsr_local_group_16 0.082 r_ncsr_local_group_1 0.077 r_ncsr_local_group_3 0.077 r_ncsr_local_group_15 0.075 r_ncsr_local_group_2 0.059 r_ncsr_local_group_7 0.049 r_ncsr_local_group_5 0.042 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19014 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing