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Crystal structure of GK2038 protein (enoyl-CoA hydratase subunit II) from Geobacillus kaustophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 15% PEG3350, 0.1M magnesium formate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 8 293 15% PEG3350, 0.09M magnesium formate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.008 α = 90 b = 117.008 β = 90 c = 117.008 γ = 90
Symmetry Space Group P 21 3
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 RIGAKU JUPITER 210 mirrors 2006-12-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2007-01-31 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.97894 SPring-8 BL26B2 2 SYNCHROTRON APS BEAMLINE 22-BM 0.97901 APS 22-BM
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 50 99.9 0.087 19.5 20.9 36275 36275 22.974
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 2.07 100 0.266 12.5 20.9 3563
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 32.45 36275 34355 1802 99.72 0.19434 0.19182 0.1925 0.24229 0.2397 RANDOM 25.016
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.288 r_dihedral_angle_4_deg 18.825 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 5.705 r_scangle_it 4.51 r_scbond_it 2.973 r_mcangle_it 1.712 r_angle_refined_deg 1.597 r_mcbond_it 1.109 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.288 r_dihedral_angle_4_deg 18.825 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 5.705 r_scangle_it 4.51 r_scbond_it 2.973 r_mcangle_it 1.712 r_angle_refined_deg 1.597 r_mcbond_it 1.109 r_nbtor_refined 0.305 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.189 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.116 r_bond_refined_d 0.017 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing