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Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 0.1M phosphate-citrate, 40%(v/v) PEG 300, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.597 α = 90 b = 114.887 β = 93.73 c = 43.429 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 315r 2010-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9801 Australian Synchrotron MX1
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 1.77 38.51 0.09 7.9 3.2 36143 3
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 1ZTG 1.77 27.16 35997 1808 100 0.1636 0.161 0.2134 0.1652 RANDOM 31.5288
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] -2.36 -1.68 1.63 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 25.703 r_dihedral_angle_3_deg 16.23 r_scangle_it 8.277 r_scbond_it 5.85 r_dihedral_angle_1_deg 5.433 r_mcangle_it 3.962 r_rigid_bond_restr 3.115 r_mcbond_it 2.409 r_angle_refined_deg 2.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 25.703 r_dihedral_angle_3_deg 16.23 r_scangle_it 8.277 r_scbond_it 5.85 r_dihedral_angle_1_deg 5.433 r_mcangle_it 3.962 r_rigid_bond_restr 3.115 r_mcbond_it 2.409 r_angle_refined_deg 2.243 r_chiral_restr 0.157 r_bond_refined_d 0.027 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2237 Nucleic Acid Atoms 388 Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction SCALA data scaling PHASER phasing