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Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V94 PDB ENTRY 1V94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 0.6M ZNSO4, 0.1M NACACODYLATE, PH6.3, pH 6.30
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.611 α = 90 b = 65.405 β = 95.28 c = 87.181 γ = 90
Symmetry Space Group P 1 21 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 2005-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.5 20 99.8 0.11 11.1 4.1 31867 -5
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 2.5 2.64 100 0.48 3.5 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1V94 2.5 86.71 30249 1607 99.7 0.199 0.196 0.2233 0.254 0.2682 RANDOM 16.8
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] -0.12 0.56 1.15 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.749 r_dihedral_angle_3_deg 23.398 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_1_deg 7.025 r_scangle_it 3.721 r_scbond_it 2.22 r_angle_refined_deg 1.785 r_mcangle_it 1.458 r_mcbond_it 0.851 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.749 r_dihedral_angle_3_deg 23.398 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_1_deg 7.025 r_scangle_it 3.721 r_scbond_it 2.22 r_angle_refined_deg 1.785 r_mcangle_it 1.458 r_mcbond_it 0.851 r_nbtor_refined 0.323 r_symmetry_hbond_refined 0.315 r_symmetry_vdw_refined 0.284 r_nbd_refined 0.25 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.143 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6451 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing