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Crystal Structure of R-alcohol dehydrogenase (RADH) (apoenyzme) from Lactobacillus brevis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HSD PDB FILE 2HSD REDUCED TO A POLY-ALA CHAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 40%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.444 α = 90 b = 85.065 β = 90 c = 115.336 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 283 IMAGE PLATE MACSCIENCE 1997-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 68.5 98.9 0.059 46.4 9.5 26474 26183 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.86 91.3 0.235 11.2 8.3
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 (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 FILE 2HSD REDUCED TO A POLY-ALA CHAIN 1.79 69.01 25103 1079 99.16 0.15112 0.15112 0.14997 0.1627 0.17819 0.1863 RANDOM 17.002
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] -0.69 0.77 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.215 r_dihedral_angle_1_deg 3.955 r_scangle_it 3.569 r_scbond_it 2.12 r_mcangle_it 1.265 r_angle_refined_deg 1.233 r_angle_other_deg 1.165 r_mcbond_it 0.669 r_nbd_refined 0.228 r_symmetry_vdw_other 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.215 r_dihedral_angle_1_deg 3.955 r_scangle_it 3.569 r_scbond_it 2.12 r_mcangle_it 1.265 r_angle_refined_deg 1.233 r_angle_other_deg 1.165 r_mcbond_it 0.669 r_nbd_refined 0.228 r_symmetry_vdw_other 0.212 r_nbd_other 0.194 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_nbtor_other r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1871 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing