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Crystal Structure of Short-Chain Dehydrogenase/Reductase of unknown Function from Caenorhabditis Elegans with Cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPX The search model was a model generated by the SWISS-MODEL server based on PDB entries 1SPX and 1RWB. experimental model PDB 1RWB The search model was a model generated by the SWISS-MODEL server based on PDB entries 1SPX and 1RWB.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 291 20% PEG 3350, 0.2M NH4F, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.19 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.69 α = 90 b = 119.69 β = 90 c = 193.22 γ = 120
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 4 Mirrors 2004-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-3 0.9746 SSRL BL11-3
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 96.1 0.067 0.067 20.9 5.5 87709 87709 1 19.6
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) 2.1 2.23 95 0.178 0.178 6.5 5.2 14412
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 The search model was a model generated by the SWISS-MODEL server based on PDB entries 1SPX and 1RWB. 2.1 34.01 86844 86844 4365 95.4 0.217 0.216 0.216 0.2122 0.245 0.242 RANDOM 25.8
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] -2.67 -0.75 -2.67 5.33
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.86 c_scbond_it 2.06 c_angle_deg 1.9 c_mcangle_it 1.78 c_improper_angle_d 1.48 c_mcbond_it 1.2 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8135 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms 192
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing CNS refinement HKL-2000 data reduction