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PfDXR - Mn2+ - NADPH - MAMK89 quaternary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JNW
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 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.518 α = 90 b = 78.201 β = 92.64 c = 111.144 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 2022-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.39 63.93 92.7 0.066 0.072 0.028 0.998 10.9 6.3 164006 17.14
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 1.39 1.41 0.97 1.116 0.537 0.582 1.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.39 63.93 155538 8391 92.62 0.16632 0.16512 0.18919 0.2192 RANDOM 23.431
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] 0.22 -0.42 0.3 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.643 r_dihedral_angle_2_deg 7.281 r_long_range_B_refined 6.55 r_long_range_B_other 6.471 r_dihedral_angle_1_deg 6.029 r_scangle_other 4.982 r_scbond_it 3.289 r_scbond_other 3.289 r_mcangle_it 3.063 r_mcangle_other 3.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.643 r_dihedral_angle_2_deg 7.281 r_long_range_B_refined 6.55 r_long_range_B_other 6.471 r_dihedral_angle_1_deg 6.029 r_scangle_other 4.982 r_scbond_it 3.289 r_scbond_other 3.289 r_mcangle_it 3.063 r_mcangle_other 3.063 r_mcbond_it 2.143 r_mcbond_other 2.142 r_angle_refined_deg 2.042 r_angle_other_deg 0.649 r_chiral_restr 0.102 r_bond_refined_d 0.012 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 659 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing