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Candida glabrata Glycogen Debranching Enzyme (GDE) in complex with Miglustat
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, SITTING DROP 7 295 0.1 M MES (pH 7), 7% v/v Tacsimate (pH 7), 20% w/v PEG MME 5K
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.078 α = 90 b = 199.274 β = 90 c = 254.213 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS EIGER X 9M 2024-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1 NSLS-II 17-ID-1
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 3.2 127.106 93.5 0.98 6.2 14.2 64558 60.61
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 3.236 3.595 0.527
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 (All) 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 3.236 127.106 36605 1857 56.69 0.237 0.2354 0.2407 0.2735 0.2773 RANDOM 86.576
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] -6.919 2.002 4.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.037 r_dihedral_angle_6_deg 11.683 r_lrange_it 7.84 r_lrange_other 7.84 r_dihedral_angle_1_deg 6.213 r_mcangle_other 3.392 r_mcangle_it 3.391 r_dihedral_angle_2_deg 3.233 r_scangle_it 2.999 r_scangle_other 2.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.037 r_dihedral_angle_6_deg 11.683 r_lrange_it 7.84 r_lrange_other 7.84 r_dihedral_angle_1_deg 6.213 r_mcangle_other 3.392 r_mcangle_it 3.391 r_dihedral_angle_2_deg 3.233 r_scangle_it 2.999 r_scangle_other 2.999 r_mcbond_it 1.921 r_mcbond_other 1.92 r_scbond_it 1.617 r_scbond_other 1.617 r_angle_refined_deg 0.858 r_angle_other_deg 0.333 r_nbd_refined 0.187 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.13 r_ncsr_local_group_1 0.125 r_symmetry_xyhbond_nbd_other 0.124 r_nbd_other 0.101 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23443 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing