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Crystal structure of short-chain alcohol dehydrogenase from hyperthermophilic archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L77 PDB ENTRY 3L77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Tris-HCl, 0.3M NaCl, PEG 3350 25%, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.18 α = 90 b = 55.5 β = 124.53 c = 82.77 γ = 90
Symmetry Space Group C 1 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 CCD MAR CCD 165 mm 2010-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.985 KURCHATOV SNC K4.4
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 1.68 30 76 0.063 18.35 62702 47643 22.724
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) 1 1.68 1.79 74.1 0.43 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3L77 1.68 26.9 62500 47643 2419 76.23 0.1476 0.1476 0.1457 0.1587 0.1808 0.1875 RANDOM 16.7643
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] -0.8 -0.4 0.08 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 22.816 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 5.925 r_angle_other_deg 2.189 r_angle_refined_deg 2.01 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 22.816 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 5.925 r_angle_other_deg 2.189 r_angle_refined_deg 2.01 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 104
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction