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Crystal structure of Acyl-coA dehydrogenase from Burkholderia thailandensis E264
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKW PDB ENTRY 1UKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Morpheus a10:
Buffer 3 pH 8.5, 0.06M divalents, 30% EDO_Peg8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.26 α = 90 b = 111 β = 90 c = 170.25 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 CCD RAYONIX MX-300 2013-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 99.1 0.096 13.6 4.8 84670 83921 12.8
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 2.26 99.4 0.456 3.6 4.9 6157
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 PDB ENTRY 1UKW 2.2 46.87 79684 4186 99.15 0.18855 0.18627 0.23162 0.2134 RANDOM 27.6
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] -1.82 -1.07 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.165 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_1_deg 6.02 r_long_range_B_refined 4.404 r_long_range_B_other 4.346 r_scangle_other 2.961 r_mcangle_other 2.172 r_mcangle_it 2.17 r_scbond_it 1.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.165 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_1_deg 6.02 r_long_range_B_refined 4.404 r_long_range_B_other 4.346 r_scangle_other 2.961 r_mcangle_other 2.172 r_mcangle_it 2.17 r_scbond_it 1.868 r_scbond_other 1.867 r_angle_refined_deg 1.54 r_mcbond_it 1.402 r_mcbond_other 1.395 r_angle_other_deg 0.849 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 11001 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 53
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling