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Crystal Structure of Human Pumilio 1 in complex with Puf5 RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M8Y PDB ENTRY 1M8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 PEG 8000, 0.05M Sodium Cacodylate pH 6.5, 0.2M KCl, 0.1M Magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.835 α = 90 b = 65.642 β = 90 c = 313.975 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 IMAGE PLATE MAR scanner 345 mm plate Si(111) monochromator 2007-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.32 50 94 0.064 18.3 3.7 33524 31513 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 84.9 0.164 5.2 2.6 2788
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M8Y 2.32 40.93 28112 3129 93.84 0.21845 0.21196 0.27678 0.2987 RANDOM 40.867
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] -0.05 2.81 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.159 r_dihedral_angle_4_deg 23.556 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_1_deg 4.731 r_scangle_it 4.077 r_scbond_it 3.056 r_angle_refined_deg 1.568 r_mcangle_it 1.567 r_mcbond_it 1.301 r_symmetry_vdw_refined 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.159 r_dihedral_angle_4_deg 23.556 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_1_deg 4.731 r_scangle_it 4.077 r_scbond_it 3.056 r_angle_refined_deg 1.568 r_mcangle_it 1.567 r_mcbond_it 1.301 r_symmetry_vdw_refined 0.361 r_nbtor_refined 0.303 r_nbd_refined 0.256 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5471 Nucleic Acid Atoms 392 Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing