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Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HLR PDB ENTRY 1HLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 278 isopropanol, magnesium chloride, HEPES, sodium arsenite, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.31 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.78 α = 90 b = 142.78 β = 90 c = 161.577 γ = 120
Symmetry Space Group P 61 2 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 4 Double crystal, Si(111) or Si(311), monochromator and toroidal mirror 2002-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 2.3 20 92.8 0.122 6.6 2.6 40781 40781 29.9
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) 2.3 2.34 91.2 0.212 3.7 2.4 1947
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1HLR 2.3 20 2 40781 39810 2047 92.78 0.208 0.207 0.18145 0.1803 0.22283 0.2212 RANDOM 26.805
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] 0.4 0.2 0.4 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 1.483 r_angle_refined_deg 1.1 r_scbond_it 0.93 r_mcangle_it 0.657 r_mcbond_it 0.353 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.92 r_scangle_it 1.483 r_angle_refined_deg 1.1 r_scbond_it 0.93 r_mcangle_it 0.657 r_mcbond_it 0.353 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6885 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling Not model building REFMAC refinement