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Structure of yeast poly(A) polymerase in a closed conformation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FA0 pdb entry 1FA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 The crystals were grown by combining the protein at 20mg/ml with an equal volume of 20% isopropanol, 20% Peg 4000, 100mM Citrate pH 5.6, and 0.1% beta mercaptoethanol, and then leaving the hanging drops for two weeks over an empty reservoir well., vapor diffusion, hanging drop
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.483 α = 90 b = 84.918 β = 111.78 c = 67.721 γ = 90
Symmetry Space Group P 1 21 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 315 2005-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
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 1.8 50 99.7 0.057 46 6.9 57072 56901
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 1.8 1.86 98.3 0.448 0.448 3.46 5.7
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 1FA0 1.8 33.04 54566 2305 99.64 0.19849 0.19698 0.1964 0.23551 0.234 RANDOM 30.965
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] -0.19 0.11 0.04 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.041 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.113 r_scangle_it 3.476 r_scbond_it 2.406 r_angle_refined_deg 1.564 r_mcangle_it 1.437 r_mcbond_it 0.994 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.041 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.113 r_scangle_it 3.476 r_scbond_it 2.406 r_angle_refined_deg 1.564 r_mcangle_it 1.437 r_mcbond_it 0.994 r_nbtor_refined 0.312 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4037 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction