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Crystal structure of the 3-ketodihydrosphingosine reductase TSC10 from Cryptococcus neoformans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.41 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.311 α = 90 b = 111.311 β = 90 c = 80.399 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER2 S 9M 2021-12-13 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 3.2 45.8 100 0.501 0.514 0.115 0.987 6.7 19.3 5219
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 3.2 3.42 100 2.87 2.945 0.655 0.711 19.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.2 45.8 4945 250 99.88 0.21328 0.21004 0.28227 0.2713 RANDOM 64.071
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] 1.05 0.53 1.05 -3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_3_deg 19.845 r_dihedral_angle_4_deg 16.962 r_long_range_B_refined 11.773 r_long_range_B_other 11.771 r_dihedral_angle_1_deg 8.518 r_scangle_other 8.409 r_mcangle_it 7.548 r_mcangle_other 7.545 r_scbond_it 5.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_3_deg 19.845 r_dihedral_angle_4_deg 16.962 r_long_range_B_refined 11.773 r_long_range_B_other 11.771 r_dihedral_angle_1_deg 8.518 r_scangle_other 8.409 r_mcangle_it 7.548 r_mcangle_other 7.545 r_scbond_it 5.292 r_scbond_other 5.22 r_mcbond_it 4.779 r_mcbond_other 4.778 r_angle_refined_deg 1.586 r_angle_other_deg 1.225 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 1549 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MrBUMP phasing