☰ Navigation Tabs
Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TIM PDB ENTRY 8TIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.1 277 PEG 6000, Tris, 2-phosphoglycolate, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.706 α = 90 b = 57.334 β = 92.89 c = 106.154 γ = 90
Symmetry Space Group C 1 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 100 CCD MARRESEARCH Bent mirror 2003-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.13 40 97.8 0.057 0.062 22 3.48 25864 25268 23.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.13 2.21 78.8 0.145 0.144 7.4 2035
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 8TIM 2.16 38.35 25268 23998 1270 96.05 0.16215 0.16215 0.16023 0.1732 0.19779 0.2143 RANDOM 11.296
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] -1.19 0.92 -1.29 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.931 r_mcangle_it 1.588 r_scangle_it 1.507 r_angle_refined_deg 1.225 r_mcbond_it 0.983 r_scbond_it 0.962 r_angle_other_deg 0.858 r_symmetry_vdw_other 0.276 r_nbd_other 0.221 r_symmetry_hbond_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.931 r_mcangle_it 1.588 r_scangle_it 1.507 r_angle_refined_deg 1.225 r_mcbond_it 0.983 r_scbond_it 0.962 r_angle_other_deg 0.858 r_symmetry_vdw_other 0.276 r_nbd_other 0.221 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.12 r_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3664 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing