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Isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila: biochemical properties and crystal structure analysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LWD PDB ENTRY 1LWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 100 MM TRIS/HCL BUFFER PH 7.4, 1.7-1.9 M AMMONIUM SULPHATE, 2% PEG 400, 60 MM MGSO4
Crystal Properties Matthews coefficient Solvent content 2.6 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.324 α = 98.9 b = 73.279 β = 98.98 c = 126.413 γ = 113.88
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 ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.75 55 86.3 0.05 9.9 2.1 162467 19.2
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 1.75 1.84 45.7 0.28 2.6 2.1
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 1LWD 1.75 20 159104 3240 86.3 0.146 0.146 0.1579 0.189 0.1979 RANDOM 15.57
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] -0.09 -0.07 -0.01 -0.02 0.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.22 r_dihedral_angle_4_deg 18.658 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.441 r_scangle_it 3.292 r_scbond_it 2.474 r_angle_refined_deg 1.638 r_mcangle_it 1.408 r_mcbond_it 1.22 r_angle_other_deg 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.22 r_dihedral_angle_4_deg 18.658 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.441 r_scangle_it 3.292 r_scbond_it 2.474 r_angle_refined_deg 1.638 r_mcangle_it 1.408 r_mcbond_it 1.22 r_angle_other_deg 0.893 r_symmetry_vdw_other 0.262 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.185 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.102 r_nbtor_other 0.086 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 12799 Nucleic Acid Atoms Solvent Atoms 1883 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing