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PfDXR - Mn2+ - SHOK314 ternary complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-HCl pH 8.0, 20%(w/v) PEG6000, and 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.763 α = 90 b = 77.554 β = 92.85 c = 111.486 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 R 4M 2024-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.01200 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.57 63.64 99.9 0.997 7.8 3.5 122920 16.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 0.544 1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.57 63.64 116554 6216 99.77 0.16867 0.16726 0.1813 0.19499 0.208 RANDOM 23.671
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] -0.42 -0.79 0.26 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.295 r_long_range_B_refined 7.41 r_long_range_B_other 7.321 r_dihedral_angle_1_deg 6.069 r_scangle_other 5.715 r_scbond_it 3.717 r_scbond_other 3.716 r_dihedral_angle_2_deg 3.517 r_mcangle_other 3.141 r_mcangle_it 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.295 r_long_range_B_refined 7.41 r_long_range_B_other 7.321 r_dihedral_angle_1_deg 6.069 r_scangle_other 5.715 r_scbond_it 3.717 r_scbond_other 3.716 r_dihedral_angle_2_deg 3.517 r_mcangle_other 3.141 r_mcangle_it 3.14 r_mcbond_it 2.073 r_mcbond_other 2.069 r_angle_refined_deg 1.938 r_angle_other_deg 0.643 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6570 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling Coot model building