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The crystal structure of the acyl-CoA dehydrogenase family protein from Porphyromonas gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 1.26M (NH4)2SO4, 0.1M Tris-HCl, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.37 63.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.34 α = 90 b = 90.34 β = 90 c = 102.069 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 ADSC QUANTUM 315 mirrors 2006-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97980 APS 19-ID
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 1.9 67.57 99.89 0.114 31.53 18.9 32189 32154 2 22.5
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 1.9 1.95 99.15 0.8 2.27 17.4 2461
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 (All) 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 1.9 67.57 32154 32154 1716 99.89 0.17498 0.17498 0.17345 0.1805 0.20541 0.2121 RANDOM 22.476
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] 0.31 0.31 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_4_deg 13.299 r_dihedral_angle_1_deg 4.451 r_scangle_it 4.213 r_scbond_it 3.12 r_mcbond_it 1.528 r_angle_other_deg 1.413 r_mcangle_it 1.382 r_angle_refined_deg 1.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_4_deg 13.299 r_dihedral_angle_1_deg 4.451 r_scangle_it 4.213 r_scbond_it 3.12 r_mcbond_it 1.528 r_angle_other_deg 1.413 r_mcangle_it 1.382 r_angle_refined_deg 1.342 r_symmetry_vdw_other 0.336 r_symmetry_hbond_refined 0.253 r_mcbond_other 0.244 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.185 r_nbd_other 0.184 r_nbtor_refined 0.176 r_chiral_restr 0.146 r_symmetry_vdw_refined 0.12 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1937 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing