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Crystal Structure of Glucose Dehydrogenase of Caenorhabditis Elegans in the Apo-Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWB Starting model was a homology model from Swiss-Model based on PDB entries 1RWB and 1G6K experimental model PDB 1G6K Starting model was a homology model from Swiss-Model based on PDB entries 1RWB and 1G6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 2M Ammonium Sulfate, 5% Isopropanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.17 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.682 α = 90 b = 89.287 β = 90 c = 108.153 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 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2004-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 2.1 50 95.4 0.086 0.086 16.4 7.7 17897 17897 1 1 19.5
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 2.1 2.18 79.4 0.239 0.239 4 1460
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 (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 Starting model was a homology model from Swiss-Model based on PDB entries 1RWB and 1G6K 2.1 19.54 1 17779 17064 834 91.5 0.203 0.202 0.202 0.2065 0.25 0.2545 RANDOM 36.6
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] -1.76 7.51 -5.74
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 3.14 c_scbond_it 2.27 c_mcangle_it 1.94 c_mcbond_it 1.28 c_angle_deg 1.2 c_improper_angle_d 0.65 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1759 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose CNS refinement SCALEPACK data scaling MOLREP phasing