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PfDXR - Mn2+ - MAMK218 ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JZ7
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 2.01 38.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.934 α = 90 b = 77.572 β = 93.2 c = 111.659 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 2022-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.33 46.04 98.8 0.995 8 3 201013
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 1.33 1.35 0.556
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 1.33 46.04 190744 10106 98.68 0.17047 0.16944 0.1694 0.18993 0.1898 RANDOM 20.789
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] -0.43 -0.19 0.28 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.621 r_long_range_B_refined 6.741 r_long_range_B_other 6.64 r_dihedral_angle_1_deg 6.059 r_scangle_other 5.071 r_scbond_it 3.23 r_scbond_other 3.229 r_mcangle_other 2.611 r_mcangle_it 2.61 r_dihedral_angle_2_deg 2.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.621 r_long_range_B_refined 6.741 r_long_range_B_other 6.64 r_dihedral_angle_1_deg 6.059 r_scangle_other 5.071 r_scbond_it 3.23 r_scbond_other 3.229 r_mcangle_other 2.611 r_mcangle_it 2.61 r_dihedral_angle_2_deg 2.425 r_angle_refined_deg 1.93 r_mcbond_it 1.75 r_mcbond_other 1.749 r_angle_other_deg 0.66 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 6518 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Coot model building Aimless data scaling REFMAC phasing