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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, 2-phosphoglycolate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.756 α = 90 b = 86.756 β = 90 c = 163.376 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 2001-05-27 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 2.6 100 99 0.109 0.095 16.5 8.7 20107 19906 19.1
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 2.59 2.69 97.5 0.392 0.382 5.2 1961
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 2.7 17.79 17698 16795 903 99.7 0.18726 0.18726 0.18465 0.1912 0.23638 0.1956 RANDOM 15.207
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] 2.18 2.18 -4.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.405 r_scangle_it 1.459 r_angle_refined_deg 1.235 r_scbond_it 1.088 r_angle_other_deg 0.778 r_mcangle_it 0.488 r_symmetry_vdw_other 0.297 r_mcbond_it 0.268 r_nbd_other 0.251 r_symmetry_hbond_refined 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.405 r_scangle_it 1.459 r_angle_refined_deg 1.235 r_scbond_it 1.088 r_angle_other_deg 0.778 r_mcangle_it 0.488 r_symmetry_vdw_other 0.297 r_mcbond_it 0.268 r_nbd_other 0.251 r_symmetry_hbond_refined 0.246 r_xyhbond_nbd_refined 0.213 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.143 r_nbtor_other 0.087 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3736 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing