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Crystal Structure of 5'-Deoxy-5'-Methylthioadenosine Phosphorylase in Complex with a Transition State Analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 6000, Spermidine, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.231 α = 90 b = 122.231 β = 90 c = 44.743 γ = 120
Symmetry Space Group P 3 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 ADSC QUANTUM 4 2001-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.98 NSLS X9B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 20 99.5 0.064 14.6 6 28021 28021 7.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 100 0.387 3.6 5.8 2794
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1CG6 1.95 20 2 28204 26776 2676 94.9 0.183 0.18 0.207 RANDOM 19.9
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] 0.24 0.86 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.19 c_scbond_it 2.15 c_mcangle_it 1.93 c_mcbond_it 1.27 c_angle_deg 1.2 c_improper_angle_d 0.79 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 25
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing