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YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LLU 1LLU.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 278 125 MM SODIUM N-TRIS(HYDROXYMETHYL)
METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8-
IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM
EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000
MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26%
MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED
IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2-
TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4,
VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.338 α = 90 b = 144.338 β = 90 c = 128.204 γ = 120
Symmetry Space Group P 3 2 1
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 MAR scanner 300 mm plate MULTIPOLE WIGGLER 1995-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.857 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 40.4 98.5 0.116 0.116 8 3.85 59662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 93.3 0.418 0.418 3.5 3.71
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LLU.PDB 2.4 28.09 58104 1473 98.54 0.17767 0.17652 0.22177 0.2223 RANDOM 40.195
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] -8.39 -8.39 16.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.239 r_dihedral_angle_4_deg 22.52 r_dihedral_angle_3_deg 18.884 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 4.147 r_long_range_B_other 4.126 r_mcangle_it 2.183 r_mcangle_other 2.183 r_scangle_other 2.151 r_angle_refined_deg 1.861
Show All KeysRMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.239 r_dihedral_angle_4_deg 22.52 r_dihedral_angle_3_deg 18.884 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 4.147 r_long_range_B_other 4.126 r_mcangle_it 2.183 r_mcangle_other 2.183 r_scangle_other 2.151 r_angle_refined_deg 1.861 r_scbond_it 1.36 r_scbond_other 1.359 r_mcbond_it 1.341 r_mcbond_other 1.341 r_angle_other_deg 0.847 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Hide All KeysNon-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10328 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 122
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement