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Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ICD PDB ENTRY 3ICD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 PEG 6K, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.569 α = 90 b = 107.569 β = 90 c = 171.143 γ = 90
Symmetry Space Group P 43 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 CCD MARRESEARCH 2003-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.9089 MAX II I711
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 2.2 39.84 0.055 17.97 4.7 51805 51735 1.35 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 2.2 2.24 100 0.497 2.91 4
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 (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 3ICD 2.2 39.84 51590 48984 2606 99.87 0.22609 0.22479 0.2215 0.25059 0.2466 RANDOM 19.407
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] -0.65 -0.65 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.575 r_scangle_it 2.427 r_scbond_it 1.553 r_angle_refined_deg 1.272 r_mcangle_it 0.761 r_mcbond_it 0.415 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.575 r_scangle_it 2.427 r_scbond_it 1.553 r_angle_refined_deg 1.272 r_mcangle_it 0.761 r_mcbond_it 0.415 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6595 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing