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Structure & function of a new Aspartylglucosaminuria variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2M NaCl, 0.1M HEPES (pH 7.5), 27% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.15 α = 90 b = 96.02 β = 90.05 c = 61.49 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 20 98.96 0.08 9.8 2 80277
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2GL9 1.5 19.99 80277 4333 98.97 0.19582 0.19429 0.22446 0.2337 RANDOM 14.216
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 6.986 r_long_range_B_refined 4.167 r_long_range_B_other 4.159 r_scangle_other 3.38 r_scbond_it 2.294 r_scbond_other 2.293 r_angle_refined_deg 2.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 14.981 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 6.986 r_long_range_B_refined 4.167 r_long_range_B_other 4.159 r_scangle_other 3.38 r_scbond_it 2.294 r_scbond_other 2.293 r_angle_refined_deg 2.214 r_mcangle_it 2.01 r_mcangle_other 2.01 r_mcbond_it 1.378 r_mcbond_other 1.355 r_angle_other_deg 1.242 r_chiral_restr 0.197 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4228 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing