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High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZI PDB ENTRY 1TZI 1HR2 experimental model PDB 1HR2 PDB ENTRY 1TZI 1HR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 34% MPD, 0.1M sodium citrate, 0.2M ammonium acetate, 25 mM magnesium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.085 α = 90 b = 53.23 β = 108.42 c = 160.555 γ = 90
Symmetry Space Group C 1 2 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 SBC-2 mirrors 2006-05-29 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-06-05 M SINGLE WAVELENGTH 3 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-06-15 M SINGLE WAVELENGTH 1,2,3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM 2 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D 3 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1,2,3 1.95 20 98.6 0.088 16.7 5.2 77127 77127
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) 1,2,3 1.95 2 95.5 0.48 1.6 2.7
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 (All) 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 1TZI 1HR2 1.95 20 77127 77127 3875 98.6 0.19632 0.19632 0.19476 0.22607 0.2539 RANDOM 35.918
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] -2.23 -0.4 0.94 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 14.991 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_1_deg 7.445 r_scangle_it 3.183 r_scbond_it 2.349 r_mcangle_it 2.092 r_angle_refined_deg 1.33 r_mcbond_it 1.271 r_angle_other_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 14.991 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_1_deg 7.445 r_scangle_it 3.183 r_scbond_it 2.349 r_mcangle_it 2.092 r_angle_refined_deg 1.33 r_mcbond_it 1.271 r_angle_other_deg 1.022 r_mcbond_other 0.326 r_nbtor_refined 0.212 r_nbd_other 0.205 r_symmetry_vdw_other 0.183 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.08 r_chiral_restr 0.059 r_metal_ion_refined 0.038 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3263 Nucleic Acid Atoms 3404 Solvent Atoms 529 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling