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X-ray crystal structure of a putative phenylacetaldehyde dehydrogenase from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CW3 PDB ENTRY 1CW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.4 uL protein @ 18 mg/mL + 0.4 uL Morpheus H3 - 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole pH 6.50, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DL-serine, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.35 63.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.62 α = 90 b = 150.07 β = 90 c = 345.91 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315r 2013-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97650 ALS 5.0.1
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 50 99.3 0.102 14.62 196538 195248 -3 22.643
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 2.05 99.6 0.482 3.13
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 1CW3 2 50 196538 195247 9833 99.34 0.1705 0.1693 0.1783 0.1929 0.1998 RANDOM 18.596
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] 0.2 0.64 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 12.682 r_dihedral_angle_1_deg 6.079 r_angle_refined_deg 1.456 r_angle_other_deg 1.149 r_mcangle_it 1.064 r_mcbond_it 0.639 r_mcbond_other 0.639 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 12.682 r_dihedral_angle_1_deg 6.079 r_angle_refined_deg 1.456 r_angle_other_deg 1.149 r_mcangle_it 1.064 r_mcbond_it 0.639 r_mcbond_other 0.639 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14931 Nucleic Acid Atoms Solvent Atoms 2003 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction