☰ Navigation Tabs
Crystal structure of a putative acyl-CoA dehydrogenase from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OIB PDB ENTRY 3OIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 EBS PACT SCEEN F12: 0.2M Sodium malonate, 0.1M Bis Tris propane pH 6.5; MYSMA.00247.B.A1 PW28486 at 27mg/ml, ph 6.5, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.93 α = 90 b = 64.75 β = 112.04 c = 83.81 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2010-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 1.7 50 96.4 0.041 20.68 4.3 88662 85434 -3 26.81
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 1.7 1.74 93.9 0.209 5.7 3.9 6578
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 3OIB 1.7 19.82 85373 4271 96.5 0.155 0.153 0.185 0.1974 RANDOM 16.71
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] -0.8 -0.16 0.51 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 11.821 r_dihedral_angle_1_deg 5.354 r_scangle_it 3.788 r_scbond_it 2.35 r_angle_refined_deg 1.563 r_mcangle_it 1.446 r_angle_other_deg 1.026 r_mcbond_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 11.821 r_dihedral_angle_1_deg 5.354 r_scangle_it 3.788 r_scbond_it 2.35 r_angle_refined_deg 1.563 r_mcangle_it 1.446 r_angle_other_deg 1.026 r_mcbond_it 0.814 r_mcbond_other 0.25 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5704 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 114
Software Software Software Name Purpose BOS data collection REFMAC refinement XDS data reduction XSCALE data scaling