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Crystal structure of Alcohol dehydrogenase zinc-binding domain protein from Burkholderia ambifaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8F 1f8f, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 RigakuReagents JCSG+ screen, A3: 20% PEG 3350, 200mM Ammonium citrate dibasic; BuamA.10611.c.B1.PS37979 at 19.1mg/ml + 2.5mM NADP (not visible in structure); cryo: 20% EG; tray 283195a3, puck kgc9-6
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.06 α = 90 b = 92.65 β = 90 c = 120.41 γ = 90
Symmetry Space Group I 2 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 RAYONIX MX-300 2016-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.7 50 97.5 0.056 0.999 19.07 6.3 47698 -3 20.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 97.8 0.477 0.921 4.02
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 1f8f, chain A 1.7 42.548 1.35 47688 2052 97.48 0.1493 0.1483 0.1488 0.1715 0.1714 RANDOM 29.138
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 14.716 f_angle_d 0.973 f_chiral_restr 0.069 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2642 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 34
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building