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PfDXR - Mn2+ - NADPH - MAMK433 quaternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JZ8
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 2.06 40.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.596 α = 90 b = 76.699 β = 92.77 c = 110.165 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 4M 2024-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.012 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 1.65 62.92 98.2 0.977 5.3 4 101361
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 1.65 1.68 0.534
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 1.65 62.92 96139 5080 98.04 0.18007 0.17867 0.1911 0.20665 0.2155 RANDOM 22.941
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] -0.67 -0.55 0.29 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.566 r_dihedral_angle_2_deg 9.298 r_long_range_B_refined 6.647 r_long_range_B_other 6.562 r_dihedral_angle_1_deg 6.363 r_scangle_other 4.868 r_scbond_it 3.057 r_scbond_other 3.057 r_mcangle_it 2.88 r_mcangle_other 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.566 r_dihedral_angle_2_deg 9.298 r_long_range_B_refined 6.647 r_long_range_B_other 6.562 r_dihedral_angle_1_deg 6.363 r_scangle_other 4.868 r_scbond_it 3.057 r_scbond_other 3.057 r_mcangle_it 2.88 r_mcangle_other 2.88 r_mcbond_it 1.873 r_mcbond_other 1.873 r_angle_refined_deg 1.745 r_angle_other_deg 0.585 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 6518 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Coot model building Aimless data scaling REFMAC phasing