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Crystal structure of THA8 in complex with Zm4 RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ME2 Apo THA8 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 14% PEG 4000 and 0.1 M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.341 α = 90 b = 90.341 β = 90 c = 81.733 γ = 90
Symmetry Space Group P 41 21 2
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 300 mm CCD 2013-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G .97856 APS 21-ID-G
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 50 100 0.05 34.4 14.1 8811 8811
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 0.944 3.3 14.7
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 Apo THA8 structure 2.8 45.21 8365 8359 415 99.9 0.207 0.205 0.2039 0.258 0.2521 RANDOM 92.1
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] -1.82 -1.82 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 17.339 r_mcangle_it 8.659 r_scbond_it 7.153 r_mcbond_it 5.963 r_mcbond_other 5.956 r_dihedral_angle_1_deg 3.125 r_angle_refined_deg 1.144 r_angle_other_deg 0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.609 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 17.339 r_mcangle_it 8.659 r_scbond_it 7.153 r_mcbond_it 5.963 r_mcbond_other 5.956 r_dihedral_angle_1_deg 3.125 r_angle_refined_deg 1.144 r_angle_other_deg 0.781 r_chiral_restr 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1500 Nucleic Acid Atoms 91 Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling