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Structure of yeast Poly(A) Polymerase in a somewhat closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 20% Peg 8000
100mM magnesium acetate
100mM imidazole pH 6.2
3% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.217 α = 90 b = 108.587 β = 90 c = 132.718 γ = 90
Symmetry Space Group P 21 21 21
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 315 2005-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
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 2.8 84 99.3 0.1 0.105 16.9 10.8 31888 31665 54
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 2.8 2.95 97.7 0.306 0.334 5.2 6.2 4216
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1FA0 2.7 65.51 31665 1664 99.83 0.19892 0.19499 0.1932 0.27508 0.2703 RANDOM 16.584
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] 0.72 0.08 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 18.926 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.963 r_angle_refined_deg 1.318 r_scbond_it 1.216 r_mcangle_it 0.832 r_mcbond_it 0.476 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.579 r_dihedral_angle_3_deg 18.926 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.963 r_angle_refined_deg 1.318 r_scbond_it 1.216 r_mcangle_it 0.832 r_mcbond_it 0.476 r_nbtor_refined 0.309 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8349 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling CNS phasing