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Crystal structure of a mutant glycosylasparaginase (G172D) that causes the genetic disease Aspartylglucosaminuria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.2M Ammonium Acetate, 0.1M Bis-Tris pH 5.5, 25% Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.04 α = 81.51 b = 52.77 β = 90.15 c = 61.89 γ = 105.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 50.15 92.6 18.8 3.8 45208
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 1.83 1.87
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1P4K 1.83 20 42925 2265 92.56 0.1577 0.15568 0.1672 0.19667 0.203 RANDOM 17.83
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] -0.68 0.45 -0.17 0.74 -0.07 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.196 r_dihedral_angle_4_deg 15.08 r_dihedral_angle_3_deg 13.24 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 5.651 r_long_range_B_other 5.507 r_scangle_other 4.103 r_scbond_it 2.672 r_scbond_other 2.669 r_mcangle_other 2.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.196 r_dihedral_angle_4_deg 15.08 r_dihedral_angle_3_deg 13.24 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 5.651 r_long_range_B_other 5.507 r_scangle_other 4.103 r_scbond_it 2.672 r_scbond_other 2.669 r_mcangle_other 2.489 r_mcangle_it 2.487 r_angle_refined_deg 1.915 r_mcbond_it 1.658 r_mcbond_other 1.651 r_angle_other_deg 1.073 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 4186 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing