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Crystal Structure of the synaptic tetramer of the G-Segment Invertase (Gin)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR4 Gin Homology Model of subunit A of 1ZR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 10% Ammonium Sulfate, 20% Ethylene Glycol, 10 mM MgSO4, 100 mM MES 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 5.33 76.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.84 α = 90 b = 116.84 β = 90 c = 117.64 γ = 120
Symmetry Space Group P 62 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 QUANTUM 315r 2006-08-06 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210r 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C 2 SYNCHROTRON ALS BEAMLINE 8.2.2 1.07210 ALS 8.2.2
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 1,2 3.5 30 99 8.59 5.7 6206 6313 3 3
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 SIRAS THROUGHOUT Gin Homology Model of subunit A of 1ZR4 3.51 46.48 5824 375 97.92 0.25894 0.2568 0.2598 0.28918 0.3004 RANDOM 146.395
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] -13.08 -6.54 -13.08 19.63
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 82.521 r_dihedral_angle_2_deg 33.388 r_dihedral_angle_3_deg 22.316 r_dihedral_angle_4_deg 13.221 r_dihedral_angle_1_deg 5.107 r_rigid_bond_restr 1.408 r_angle_refined_deg 0.988 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 82.521 r_dihedral_angle_2_deg 33.388 r_dihedral_angle_3_deg 22.316 r_dihedral_angle_4_deg 13.221 r_dihedral_angle_1_deg 5.107 r_rigid_bond_restr 1.408 r_angle_refined_deg 0.988 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 984 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement XDS data reduction XDS data scaling