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Crystal structure of a small-chain dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5I PDB entry 1O5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M ammonium acetate, 10% PEG 3350, 0.2 M BIS-TRIS pH 6.5, Protein concentration: 8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.36 α = 90 b = 122.89 β = 111.09 c = 63.14 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2011-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
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 2.347 45 97 0.182 10.57 3.72 35379 34318 -3 29.17
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 2.35 2.49 94.3 0.709 2.74 3.56 5671
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 THROUGHOUT PDB entry 1O5I 2.347 42.524 2 35379 34312 1712 97.26 0.1823 0.1808 0.1795 0.2099 0.2067 Random 36.63
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] -3.7327 -5.9908 4.0418 -0.3091
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.316 f_angle_d 0.667 f_chiral_restr 0.038 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5615 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling