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Crystal structure of apo alpha-galactosidase A at pH 4.5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.82 56.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.375 α = 90 b = 90.375 β = 90 c = 217.524 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 3.01 78 18676
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 3.01 44.66 18676 971 88.08 0.239 0.236 0.2294 0.301 0.2924 RANDOM 121.193
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] 4.48 2.24 4.48 -6.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.224 r_dihedral_angle_3_deg 23.591 r_dihedral_angle_4_deg 23.071 r_dihedral_angle_1_deg 7.568 r_angle_refined_deg 1.844 r_scangle_it 1.606 r_scbond_it 1.033 r_mcangle_it 0.63 r_symmetry_vdw_refined 0.484 r_mcbond_it 0.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.224 r_dihedral_angle_3_deg 23.591 r_dihedral_angle_4_deg 23.071 r_dihedral_angle_1_deg 7.568 r_angle_refined_deg 1.844 r_scangle_it 1.606 r_scbond_it 1.033 r_mcangle_it 0.63 r_symmetry_vdw_refined 0.484 r_mcbond_it 0.388 r_symmetry_hbond_refined 0.37 r_nbtor_refined 0.328 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6244 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction