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Crystal Structure of The Za Domain bound to Z-RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QBJ PDB entry: 1QBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.6 292 40% PEG600, 100mM Sodium Acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.603 α = 90 b = 92.776 β = 90 c = 50.229 γ = 90
Symmetry Space Group C 2 2 21
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 2005-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97 APS 19-ID
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 2.25 25 90.7 0.075 5.1 7511
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) 2.25 2.308 92.5 0.197 5.1
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: 1QBJ 2.25 25 7499 6769 730 88.47 0.19908 0.19436 0.2009 0.24392 0.2434 RANDOM 19.895
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] -0.93 -1.01 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.482 r_dihedral_angle_4_deg 25.514 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_1_deg 4.848 r_scangle_it 2.985 r_angle_other_deg 2.783 r_scbond_it 1.868 r_mcangle_it 1.36 r_angle_refined_deg 1.198 r_mcbond_it 0.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.482 r_dihedral_angle_4_deg 25.514 r_dihedral_angle_3_deg 18.361 r_dihedral_angle_1_deg 4.848 r_scangle_it 2.985 r_angle_other_deg 2.783 r_scbond_it 1.868 r_mcangle_it 1.36 r_angle_refined_deg 1.198 r_mcbond_it 0.705 r_symmetry_vdw_refined 0.256 r_symmetry_vdw_other 0.233 r_nbd_refined 0.21 r_nbd_other 0.209 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.101 r_nbtor_other 0.099 r_metal_ion_refined 0.094 r_chiral_restr 0.053 r_mcbond_other 0.025 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 968 Nucleic Acid Atoms 277 Solvent Atoms 157 Heterogen Atoms 3
Software Software Software Name Purpose SCALA data scaling EPMR phasing REFMAC refinement PDB_EXTRACT data extraction CCP4 data scaling