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PfDXR - Mn2+ - SHOK317 - 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 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.652 α = 90 b = 78.016 β = 92.94 c = 111.145 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 2M 2024-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 1.69 51.58 99.9 0.995 6.7 4.1 98579 15.29
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 1.69 1.72 0.525 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 1.69 51.58 93432 5091 99.86 0.1697 0.16828 0.1797 0.19557 0.2038 RANDOM 24.078
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] -0.08 -0.17 0.22 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.583 r_dihedral_angle_2_deg 7.707 r_long_range_B_refined 6.886 r_long_range_B_other 6.802 r_dihedral_angle_1_deg 6.099 r_scangle_other 4.792 r_mcangle_it 3.021 r_mcangle_other 3.02 r_scbond_it 2.987 r_scbond_other 2.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.583 r_dihedral_angle_2_deg 7.707 r_long_range_B_refined 6.886 r_long_range_B_other 6.802 r_dihedral_angle_1_deg 6.099 r_scangle_other 4.792 r_mcangle_it 3.021 r_mcangle_other 3.02 r_scbond_it 2.987 r_scbond_other 2.986 r_mcbond_it 1.913 r_mcbond_other 1.911 r_angle_refined_deg 1.72 r_angle_other_deg 0.577 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 6570 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling Coot model building