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Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GO4 PDB entry 4GO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 Morpheus(c3): glycerol, peg4000, sodium nitrate, sodium phosphate, ammonium sulfate, imidazole, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.13 α = 90 b = 125.61 β = 90 c = 150.85 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2013-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97857 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 1.9 50 99.9 0.107 15.56 7.5 167640 167523 -3
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 99.8 0.48 4.39
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 (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 PDB entry 4GO4 1.9 19.86 175674 158858 8408 99.83 0.15218 0.15061 0.1624 0.18209 0.1906 RANDOM 14.272
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] 0.05 -0.1 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 5.906 r_angle_refined_deg 1.441 r_scbond_it 0.916 r_mcangle_it 0.837 r_angle_other_deg 0.802 r_mcbond_it 0.484 r_mcbond_other 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 19.144 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 5.906 r_angle_refined_deg 1.441 r_scbond_it 0.916 r_mcangle_it 0.837 r_angle_other_deg 0.802 r_mcbond_it 0.484 r_mcbond_other 0.484 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14700 Nucleic Acid Atoms Solvent Atoms 2161 Heterogen Atoms 184
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction