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PfDXR - Mn2+ - SHOK314 - NADPH quaternary complex
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 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.578 α = 90 b = 76.876 β = 92.54 c = 111.148 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 2024-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 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 1.58 45.01 96 0.991 6.2 3.1 114534 16.32
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 1.58 1.6 0.505 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.58 45.01 108547 5807 95.88 0.16416 0.163 0.1774 0.18567 0.1983 RANDOM 24.954
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] -0.05 -0.94 0.64 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.692 r_dihedral_angle_2_deg 8.693 r_long_range_B_refined 7.417 r_long_range_B_other 7.369 r_dihedral_angle_1_deg 6.077 r_scangle_other 5.645 r_scbond_it 3.592 r_scbond_other 3.592 r_mcangle_other 3.147 r_mcangle_it 3.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.692 r_dihedral_angle_2_deg 8.693 r_long_range_B_refined 7.417 r_long_range_B_other 7.369 r_dihedral_angle_1_deg 6.077 r_scangle_other 5.645 r_scbond_it 3.592 r_scbond_other 3.592 r_mcangle_other 3.147 r_mcangle_it 3.146 r_mcbond_it 2.069 r_mcbond_other 2.069 r_angle_refined_deg 1.873 r_angle_other_deg 0.616 r_chiral_restr 0.096 r_bond_refined_d 0.011 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 475 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling Coot model building