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Crystal structure of aldehyde dehydrogenase from Burkholderia xenovorans LB400
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QI1 PDB ENTRY 1QI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6
Crystal Properties Matthews coefficient Solvent content 2.14 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.98 α = 111.18 b = 67.69 β = 90.48 c = 77.62 γ = 113.27
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RAXIS 4 MIRRORS 2007-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.6 46.31 92.6 0.06 10.4 3.67 121689 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 1.6 1.66 88.1 0.36 2.5 3.17
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QI1 1.6 37.82 115520 6128 92.6 0.209 0.207 0.2046 0.238 0.2366 RANDOM 18.32
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.771 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.398 r_scangle_it 2.901 r_scbond_it 1.87 r_angle_refined_deg 1.481 r_mcangle_it 1.031 r_mcbond_it 0.657 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.771 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.398 r_scangle_it 2.901 r_scbond_it 1.87 r_angle_refined_deg 1.481 r_mcangle_it 1.031 r_mcbond_it 0.657 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.141 r_symmetry_hbond_refined 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 7723 Nucleic Acid Atoms Solvent Atoms 736 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing