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Crystal structure of a RNA binding domain of polyadenylate-binding protein (PABPN1) from Homo sapiens at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 2.0M (NH4)2SO4, 2.0% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.35 63.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.678 α = 90 b = 92.678 β = 90 c = 92.678 γ = 90
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 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2011-07-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97925,0.97894 SSRL BL11-1
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 1.95 29.307 99.2 0.045 18.08 9771 -3 37.166
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 1.95 2.02 97.2 0.771 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.95 29.307 9767 470 99.51 0.165 0.1629 0.2096 0.2145 RANDOM 53.3522
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_3_deg 15.035 r_torsion_it 11.522 r_dihedral_angle_4_deg 9.444 r_angle_it 8.617 r_bond_it 6.535 r_angle_others 5.182 r_dihedral_angle_1_deg 4.427 r_angle_refined_deg 1.714 r_bond_other 1.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_3_deg 15.035 r_torsion_it 11.522 r_dihedral_angle_4_deg 9.444 r_angle_it 8.617 r_bond_it 6.535 r_angle_others 5.182 r_dihedral_angle_1_deg 4.427 r_angle_refined_deg 1.714 r_bond_other 1.586 r_angle_other_deg 0.995 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 677 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 30
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing