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Crystal structure of isocitrate dehydrogenase from Campylobacter corcagiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Li2SO4, 0.1 M Tris pH8.5, 40% PEG400
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.501 α = 90 b = 92.694 β = 90 c = 147.321 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18067 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 49.11 99.9 0.125 0.036 0.999 18.3 13.1 30370
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.978 0.272 0.856 3.1
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 1ITW 2.5 48.93 28767 1548 99.88 0.1919 0.1882 0.1979 0.2589 0.2623 RANDOM 46.011
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 -1.58 3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 18.587 r_dihedral_angle_3_deg 17.762 r_dihedral_angle_1_deg 7.574 r_angle_refined_deg 1.724 r_angle_other_deg 1.257 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 18.587 r_dihedral_angle_3_deg 17.762 r_dihedral_angle_1_deg 7.574 r_angle_refined_deg 1.724 r_angle_other_deg 1.257 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5706 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing