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PfDXR - Mn2+ - MAMK89 ternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JNV
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 1.98 37.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.637 α = 90 b = 77.022 β = 92.67 c = 111.275 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 PILATUS3 S 6M 2022-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 63.31 97 0.057 0.07 0.039 0.984 11.6 3.3 134944 14.6
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 1.5 1.53 0.657 0.806 0.46 0.528 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 1.5 63.31 128254 6686 96.97 0.17248 0.17103 0.1715 0.20052 0.2007 RANDOM 22.324
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] -0.45 -0.35 0.65 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.795 r_long_range_B_refined 6.73 r_long_range_B_other 6.658 r_dihedral_angle_1_deg 5.954 r_scangle_other 4.889 r_scbond_it 3.108 r_scbond_other 3.107 r_mcangle_it 2.755 r_mcangle_other 2.755 r_dihedral_angle_2_deg 2.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.795 r_long_range_B_refined 6.73 r_long_range_B_other 6.658 r_dihedral_angle_1_deg 5.954 r_scangle_other 4.889 r_scbond_it 3.108 r_scbond_other 3.107 r_mcangle_it 2.755 r_mcangle_other 2.755 r_dihedral_angle_2_deg 2.318 r_mcbond_it 1.867 r_mcbond_other 1.866 r_angle_refined_deg 1.859 r_angle_other_deg 0.623 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 582 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing