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Crystal structure of KRED mutant-Y199A/N149L
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 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.486 α = 90 b = 122.45 β = 93.52 c = 141.429 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 80 PIXEL DECTRIS PILATUS3 6M 2024-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2 122.45 99.8 0.056 0.062 0.026 0.999 14.4 5.2 149684
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 2.03 99.2 0.66 0.755 0.361 0.831 3.9
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 92.67 142046 7535 99.71 0.20695 0.20565 0.2113 0.23224 0.2354 RANDOM 45.71
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] 0.3 -2.65 -3.32 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_4_deg 12.653 r_long_range_B_refined 7.741 r_long_range_B_other 7.74 r_dihedral_angle_1_deg 6.508 r_scangle_other 6.293 r_mcangle_it 5.12 r_mcangle_other 5.12 r_scbond_it 4.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_4_deg 12.653 r_long_range_B_refined 7.741 r_long_range_B_other 7.74 r_dihedral_angle_1_deg 6.508 r_scangle_other 6.293 r_mcangle_it 5.12 r_mcangle_other 5.12 r_scbond_it 4.514 r_scbond_other 4.505 r_mcbond_it 3.957 r_mcbond_other 3.957 r_angle_refined_deg 1.466 r_angle_other_deg 1.308 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 14888 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 461
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing