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Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 EDTA, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.43 63.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.488 α = 90 b = 109.488 β = 90 c = 187.58 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 4 graphite 2003-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0781 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.4 80 93.7 6744 6322 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.486 81.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.4 20 6744 5636 322 96.96 0.31 0.30601 0.30486 0.2799 0.32706 0.265 RANDOM 40.392
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] -2.34 -1.17 -2.34 3.51
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.322 r_scbond_it 7.12 r_mcangle_it 6.31 r_mcbond_it 3.632 r_dihedral_angle_1_deg 2.815 r_angle_refined_deg 0.937 r_symmetry_hbond_refined 0.686 r_symmetry_vdw_refined 0.469 r_nbd_refined 0.129 r_xyhbond_nbd_refined 0.101
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.322 r_scbond_it 7.12 r_mcangle_it 6.31 r_mcbond_it 3.632 r_dihedral_angle_1_deg 2.815 r_angle_refined_deg 0.937 r_symmetry_hbond_refined 0.686 r_symmetry_vdw_refined 0.469 r_nbd_refined 0.129 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 759 Nucleic Acid Atoms 1489 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing