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Crystal structure of KRED
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A4XEP2-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M sodium citrate; Tris pH 7.0; NaCl
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.446 α = 90 b = 121.878 β = 90 c = 143.281 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2025-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 2.53 71.74 99.7 0.215 0.231 0.082 0.983 5.6 7.5 39420
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 2.53 2.63 100 0.687 0.736 0.258 0.876 7.7
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 MOLECULAR REPLACEMENT THROUGHOUT 2.53 71.74 37314 1995 99.19 0.21559 0.21235 0.2163 0.27498 0.2739 RANDOM 53.685
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] -2.07 -4.27 6.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.096 r_dihedral_angle_3_deg 19.859 r_dihedral_angle_4_deg 18.898 r_long_range_B_refined 11.491 r_long_range_B_other 11.491 r_dihedral_angle_1_deg 7.425 r_scangle_other 7.302 r_mcangle_it 6.931 r_mcangle_other 6.931 r_scbond_it 4.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.096 r_dihedral_angle_3_deg 19.859 r_dihedral_angle_4_deg 18.898 r_long_range_B_refined 11.491 r_long_range_B_other 11.491 r_dihedral_angle_1_deg 7.425 r_scangle_other 7.302 r_mcangle_it 6.931 r_mcangle_other 6.931 r_scbond_it 4.929 r_scbond_other 4.929 r_mcbond_it 4.785 r_mcbond_other 4.782 r_angle_refined_deg 1.582 r_angle_other_deg 1.276 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7449 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing