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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 3 59.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.327 α = 90 b = 88.327 β = 90 c = 163.874 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 IMAGE PLATE MARRESEARCH Focusing mirror 2002-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS 1.5
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 2.8 20 99.7 0.089 0.11 25 5.11 16713 16663 21.4
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 2.8 2.9 97.4 0.6 0.74 3.4 1622
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 19.96 14272 13881 727 97.26 0.20663 0.20663 0.20473 0.1832 0.24433 0.2384 RANDOM 14.592
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] 1.57 1.57 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.645 r_scangle_it 1.532 r_angle_other_deg 1.329 r_angle_refined_deg 1.328 r_scbond_it 0.944 r_mcangle_it 0.509 r_symmetry_vdw_other 0.302 r_mcbond_it 0.278 r_nbd_other 0.247 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.645 r_scangle_it 1.532 r_angle_other_deg 1.329 r_angle_refined_deg 1.328 r_scbond_it 0.944 r_mcangle_it 0.509 r_symmetry_vdw_other 0.302 r_mcbond_it 0.278 r_nbd_other 0.247 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.09 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 3742 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing