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Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IXA PDB ENTRY 2IXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.25 46-50% 2-METHYL-2,4-PENTANEDIOL (MPD), 75 MM NA-CITRATE PH 6.25
Crystal Properties Matthews coefficient Solvent content 3.44 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.189 α = 90 b = 88.189 β = 90 c = 301.438 γ = 120
Symmetry Space Group P 65 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 CCD ADSC CCD 2004-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 40 98.2 0.05 33.7 12.3 27626 43.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 84.3 0.26 9.4 7.8
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 PDB ENTRY 2IXA 2.4 20 26303 1111 97.9 0.174 0.173 0.1922 0.2 0.2133 RANDOM 40.62
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] 2.85 1.43 2.85 -4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 16.313 r_dihedral_angle_1_deg 5.471 r_scangle_it 1.386 r_angle_refined_deg 1.141 r_scbond_it 0.911 r_angle_other_deg 0.85 r_mcangle_it 0.491 r_mcbond_it 0.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 16.313 r_dihedral_angle_1_deg 5.471 r_scangle_it 1.386 r_angle_refined_deg 1.141 r_scbond_it 0.911 r_angle_other_deg 0.85 r_mcangle_it 0.491 r_mcbond_it 0.425 r_symmetry_vdw_other 0.332 r_nbd_other 0.19 r_nbd_refined 0.18 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.134 r_nbtor_other 0.083 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3402 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling