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PfDXR - Mn2+ - NADPH - MAMK251 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 1.99 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.464 α = 90 b = 77.52 β = 92.19 c = 111.475 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 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.77 40.43 99.7 0.997 9.5 3.3 85099
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 1.77 1.8 0.526
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 1.77 40.43 80575 4452 99.6 0.17083 0.16904 0.1797 0.20294 0.2127 RANDOM 32.564
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] -0.23 -0.24 0.49 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.568 r_dihedral_angle_2_deg 8.364 r_long_range_B_refined 7.151 r_long_range_B_other 7.107 r_dihedral_angle_1_deg 6.386 r_scangle_other 5.194 r_scbond_it 3.335 r_scbond_other 3.334 r_mcangle_it 3.099 r_mcangle_other 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.568 r_dihedral_angle_2_deg 8.364 r_long_range_B_refined 7.151 r_long_range_B_other 7.107 r_dihedral_angle_1_deg 6.386 r_scangle_other 5.194 r_scbond_it 3.335 r_scbond_other 3.334 r_mcangle_it 3.099 r_mcangle_other 3.099 r_mcbond_it 2.111 r_mcbond_other 2.11 r_angle_refined_deg 1.694 r_angle_other_deg 0.565 r_chiral_restr 0.085 r_bond_refined_d 0.008 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 421 Heterogen Atoms 169
Software Software Software Name Purpose xia2 data reduction Coot model building REFMAC refinement