☰ 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 5.5 294 citrate, ammonium sulphate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.97 58.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.422 α = 90 b = 88.422 β = 90 c = 161.874 γ = 90
Symmetry Space Group P 41 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 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 2.9 19.73 98.8 0.105 0.095 15.1 5.41 20463 20217 31.1
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 2.9 99.4 0.298 0.355 7.1 2007
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 2.9 19.7 14760 13996 764 99.24 0.15794 0.15794 0.15611 0.1554 0.19287 0.1885 RANDOM 25.34
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_1_deg 6.04 r_scangle_it 1.684 r_angle_refined_deg 1.188 r_scbond_it 0.938 r_angle_other_deg 0.76 r_mcangle_it 0.537 r_mcbond_it 0.261 r_nbd_other 0.229 r_symmetry_vdw_other 0.228 r_xyhbond_nbd_refined 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.04 r_scangle_it 1.684 r_angle_refined_deg 1.188 r_scbond_it 0.938 r_angle_other_deg 0.76 r_mcangle_it 0.537 r_mcbond_it 0.261 r_nbd_other 0.229 r_symmetry_vdw_other 0.228 r_xyhbond_nbd_refined 0.218 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.109 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.084 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3742 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing