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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 3GVO PDB ENTRY 3GVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.2M ammonium citrate, 0.2M Li2SO4, 22%(w/v) PEG 4000 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.54 α = 90 b = 150.54 β = 90 c = 77.22 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 ADSC QUANTUM 315 2008-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.92 Diamond I03
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 2.8 37.88 99.9 0.089 11.5 5.4 24770 24746 5.7 75.5
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 2.8 2.95 100 0.471 5.7 5.5 3595
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 (All) 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 3GVO 2.8 37.87 23492 23335 1250 99.33 0.19457 0.19457 0.19151 0.1888 0.25317 0.2473 RANDOM 63.549
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 0.09 0.19 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.121 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 4.904 r_scangle_it 2.168 r_angle_refined_deg 1.328 r_scbond_it 1.29 r_mcangle_it 0.935 r_mcbond_it 0.53 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.121 r_dihedral_angle_4_deg 20.462 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 4.904 r_scangle_it 2.168 r_angle_refined_deg 1.328 r_scbond_it 1.29 r_mcangle_it 0.935 r_mcbond_it 0.53 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.23 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5552 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 20
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling