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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 5.2 295 PEG 6000, citrate, t-butanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.67 α = 90 b = 61.67 β = 90 c = 500.886 γ = 120
Symmetry Space Group P 61 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 MARRESEARCH Bent mirror 2002-06-15 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) 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 2.8 30 94.3 0.083 10.42 6.62 16236 15311 20.4
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 2.76 2.93 82.4 0.117 7 5.29 2572
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 2.85 28.28 13977 13279 698 100 0.20468 0.20468 0.20214 0.188 0.25185 0.2381 RANDOM 3.209
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] 1.41 0.71 1.41 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.193 r_angle_refined_deg 1.074 r_angle_other_deg 0.837 r_scangle_it 0.488 r_scbond_it 0.293 r_nbd_other 0.212 r_symmetry_vdw_other 0.171 r_mcangle_it 0.165 r_nbd_refined 0.159 r_xyhbond_nbd_refined 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.193 r_angle_refined_deg 1.074 r_angle_other_deg 0.837 r_scangle_it 0.488 r_scbond_it 0.293 r_nbd_other 0.212 r_symmetry_vdw_other 0.171 r_mcangle_it 0.165 r_nbd_refined 0.159 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.099 r_mcbond_it 0.089 r_symmetry_hbond_refined 0.082 r_nbtor_other 0.078 r_chiral_restr 0.05 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3744 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing