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Crystal structure of DNA aptamer C8N5t in complex with Plasmodium falciparum lactate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M sodium citrate pH 5.5, 15% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.106 α = 90 b = 105.572 β = 90 c = 158.992 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2024-12-15 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) 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 1.95 87.95 92.5 0.347 6.5 13 55431
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 1.95 2.21 1.56
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 FREE R-VALUE 2.1 87.949 54446 2730 59.801 0.205 0.2022 0.2091 0.2666 0.2671 21.548
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] -0.211 -0.139 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.092 r_dihedral_angle_6_deg 14.702 r_dihedral_angle_2_deg 7.423 r_dihedral_angle_1_deg 6.476 r_lrange_it 4.628 r_lrange_other 4.628 r_scangle_it 3.599 r_scangle_other 3.598 r_mcangle_it 2.403 r_mcangle_other 2.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.092 r_dihedral_angle_6_deg 14.702 r_dihedral_angle_2_deg 7.423 r_dihedral_angle_1_deg 6.476 r_lrange_it 4.628 r_lrange_other 4.628 r_scangle_it 3.599 r_scangle_other 3.598 r_mcangle_it 2.403 r_mcangle_other 2.403 r_scbond_it 2.225 r_scbond_other 2.225 r_angle_refined_deg 1.679 r_mcbond_it 1.468 r_mcbond_other 1.466 r_angle_other_deg 0.538 r_dihedral_angle_other_2_deg 0.535 r_nbd_refined 0.221 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.175 r_nbd_other 0.156 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_xyhbond_nbd_other 0.052 r_symmetry_xyhbond_nbd_other 0.029 r_chiral_restr_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9307 Nucleic Acid Atoms 661 Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing