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Structure and RNA binding of the mouse Pumilio-2 Puf Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IB2 PDB ENTRY 1ib2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 0.2M ammonium citrate, 20%(w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.393 α = 90 b = 142.393 β = 90 c = 112.233 γ = 120
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 MARMOSAIC 225 mm CCD 2008-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.05 SRS PX10.1
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 1.6 83.045 98.3 0.067 15 5.4 57386 56410 1.7 19.609
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 1.6 1.69 92.3 0.393 1.7 2 7642
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 (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 1ib2 1.6 32.72 57413 56219 2866 97.9 0.168 0.167 0.1691 0.198 0.1989 RANDOM 27.82
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] 0.44 0.22 0.44 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.652 r_dihedral_angle_4_deg 17.455 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 4.7 r_scangle_it 3.883 r_scbond_it 2.432 r_mcangle_it 1.371 r_angle_refined_deg 1.347 r_mcbond_it 0.945 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.652 r_dihedral_angle_4_deg 17.455 r_dihedral_angle_3_deg 12.63 r_dihedral_angle_1_deg 4.7 r_scangle_it 3.883 r_scbond_it 2.432 r_mcangle_it 1.371 r_angle_refined_deg 1.347 r_mcbond_it 0.945 r_nbtor_refined 0.309 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.176 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2776 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 32
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction