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Crystal structure of 3-isopropylmalate dehydrogenase (Saci_0600) from Sulfolobus acidocaldarius complex with 3-isopropylmalate and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.0 M Ammonium sulfate, 0.1 M Cacodylate (pH6.5), 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.024 α = 90 b = 136.719 β = 90 c = 112.519 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2012-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.7 17.9 7.3 35126
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1A05 2.2 33.51 33237 1755 99.61 0.19306 0.19014 0.24961 0.2306 RANDOM 24.169
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] 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.759 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 17.598 r_dihedral_angle_1_deg 6.191 r_long_range_B_refined 4.542 r_long_range_B_other 4.501 r_scangle_other 3.244 r_mcangle_other 2.055 r_mcangle_it 2.054 r_scbond_it 1.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.759 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 17.598 r_dihedral_angle_1_deg 6.191 r_long_range_B_refined 4.542 r_long_range_B_other 4.501 r_scangle_other 3.244 r_mcangle_other 2.055 r_mcangle_it 2.054 r_scbond_it 1.974 r_scbond_other 1.962 r_angle_refined_deg 1.438 r_mcbond_it 1.295 r_mcbond_other 1.293 r_angle_other_deg 0.841 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing