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Structural basis of glycine amide on suppression of protein aggregation by high resolution X-ray analysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L PDB ENTRY 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Batch 4.5 293 0.05M sodium acetate, 1.0M glycine amide, pH 4.5, Batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.51 α = 90 b = 78.51 β = 90 c = 36.962 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE RIGAKU RAXIS V mirrors 2010-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.000 SPring-8 BL32B2
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 1.05 50 0.039 6.8 102269
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) 1.05 1.09 94 0.308 5.5 3.5
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 193L 1.05 30 51208 2738 99.27 0.14674 0.1459 0.1438 0.16306 0.1617 RANDOM 14.174
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 12.437 r_sphericity_free 11.498 r_sphericity_bonded 7.253 r_dihedral_angle_1_deg 6.228 r_scangle_it 5.099 r_scbond_it 3.819 r_mcangle_it 3.21 r_mcbond_it 2.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 18.176 r_dihedral_angle_3_deg 12.437 r_sphericity_free 11.498 r_sphericity_bonded 7.253 r_dihedral_angle_1_deg 6.228 r_scangle_it 5.099 r_scbond_it 3.819 r_mcangle_it 3.21 r_mcbond_it 2.234 r_rigid_bond_restr 2.129 r_angle_refined_deg 2.006 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.175 r_metal_ion_refined 0.17 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling