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Structure of Yeast Poly(A) Polymerase with ATP and oligo(A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HHP PDB Entry: 2HHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 273 .1M bis tris propane pH 6.4, .2M Li acetate, 16% Peg 3350, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.633 α = 90 b = 85.907 β = 90 c = 107.469 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 2006-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 30 95.7 0.072 12.8 12 56633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 76 0.275 7.5 4438
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 PDB Entry: 2HHP 1.8 29.71 56560 2896 95.62 0.191 0.189 0.1873 0.225 0.2225 RANDOM 28.984
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.465 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 5.456 r_scangle_it 2.548 r_scbond_it 1.762 r_angle_refined_deg 1.244 r_mcangle_it 1.121 r_mcbond_it 0.825 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.465 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 5.456 r_scangle_it 2.548 r_scbond_it 1.762 r_angle_refined_deg 1.244 r_mcangle_it 1.121 r_mcbond_it 0.825 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4330 Nucleic Acid Atoms 110 Solvent Atoms 509 Heterogen Atoms 100
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing