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Pseudomonas aeruginosa DapD (PA3666) in complex with CoA and succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RIJ polyAla model of 2RIJ.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.47 64.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.282 α = 90 b = 123.282 β = 90 c = 198.763 γ = 90
Symmetry Space Group P 41 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 4r 2009-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 66 100 0.113 0.113 17.1 6.6 60616 60616 42.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.654 0.654 2.6 6.7 8713
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT polyAla model of 2RIJ.pdb 2.4 53.13 57431 57431 3101 99.99 0.22627 0.22671 0.22454 0.2194 0.26748 0.2556 RANDOM 22.91
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 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.745 r_dihedral_angle_4_deg 27.462 r_dihedral_angle_3_deg 17.83 r_dihedral_angle_1_deg 6.468 r_scangle_it 2.824 r_scbond_it 1.644 r_angle_refined_deg 1.425 r_mcangle_it 1.114 r_angle_other_deg 0.887 r_mcbond_it 0.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.745 r_dihedral_angle_4_deg 27.462 r_dihedral_angle_3_deg 17.83 r_dihedral_angle_1_deg 6.468 r_scangle_it 2.824 r_scbond_it 1.644 r_angle_refined_deg 1.425 r_mcangle_it 1.114 r_angle_other_deg 0.887 r_mcbond_it 0.579 r_mcbond_other 0.142 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7459 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 168
Software Software Software Name Purpose MxCuBE data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling