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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 8.5 293 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.738 α = 90 b = 118.817 β = 90 c = 121.279 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 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 1.78 121.28 100 0.088 0.092 0.028 0.999 15.9 10.8 87610
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 1.78 1.81 100 0.945 0.989 0.292 0.917 11.3
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 1.78 84.87 83186 4322 99.96 0.16523 0.16362 0.1738 0.19654 0.202 RANDOM 28.303
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] 2.34 -0.2 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_4_deg 11.484 r_long_range_B_refined 7.145 r_long_range_B_other 7.134 r_dihedral_angle_1_deg 6.314 r_scangle_other 5.389 r_scbond_it 3.737 r_scbond_other 3.736 r_mcangle_it 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.547 r_dihedral_angle_3_deg 13.536 r_dihedral_angle_4_deg 11.484 r_long_range_B_refined 7.145 r_long_range_B_other 7.134 r_dihedral_angle_1_deg 6.314 r_scangle_other 5.389 r_scbond_it 3.737 r_scbond_other 3.736 r_mcangle_it 3.001 r_mcangle_other 3.001 r_mcbond_it 2.312 r_mcbond_other 2.311 r_angle_refined_deg 1.514 r_angle_other_deg 1.448 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 7429 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 196
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing REFMAC refinement