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Crystal Structure of putative Tropinone Reductase-II from Caenorhabditis Elegans with Cofactor and Substrate
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, SITTING DROP 6 291 65% MPD, 0.1M Mes, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.589 α = 90 b = 109.589 β = 90 c = 162.591 γ = 90
Symmetry Space Group P 41 21 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 2004-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.4 50 99.2 0.084 0.084 12.3 5.2 39301 39301 1 1 37.5
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 2.4 2.49 96.3 0.323 0.323 2 4 3739
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. 2.4 27.17 37486 37486 1862 95.1 0.192 0.191 0.191 0.1865 0.215 0.2105 RANDOM 40.9
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] -2.49 -2.49 4.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 2.86 c_scbond_it 1.99 c_angle_deg 1.9 c_mcangle_it 1.58 c_improper_angle_d 1.51 c_mcbond_it 1.01 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.2 c_scangle_it 2.86 c_scbond_it 1.99 c_angle_deg 1.9 c_mcangle_it 1.58 c_improper_angle_d 1.51 c_mcbond_it 1.01 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4068 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 116
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing