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Benzaldehyde Dehydrogenase, a Class 3 Aldehyde Dehydrogenase, with bound NADP+ and Benzoate Adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2.0 M Ammonium sulfate, 5% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 3.23 61.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.003 α = 90 b = 195.003 β = 90 c = 129.065 γ = 90
Symmetry Space Group I 41 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 MAR CCD 165 mm MONOCHROMATOR AND MIRRORS 2006-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.28 50 99.5 0.179 0.185 0.052 5.8 14.2 56492 34.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.33 97.2 0.785 11.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3LV1 2.28 34.865 1.35 56464 2826 99.47 0.192 0.1898 0.1962 0.2339 0.2312 RANDOM 29.471
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 f_dihedral_angle_d 14.154 f_angle_d 0.796 f_chiral_restr 0.031 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6692 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction HKL-2000 data reduction