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X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CZW another crystal form (pdb id 3czw)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 1.7 M ammonium sulphate, 50 mM cacodylate buffer, 15 mM magnesium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.653 α = 90 b = 46.653 β = 90 c = 126.397 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 100 CCD MAR CCD 165 mm 2004-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8020 EMBL/DESY, HAMBURG X13
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 20 99.8 0.055 37 10.6 3434 3434 29
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 2.03 100 0.463 4.7 8.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT another crystal form (pdb id 3czw) 2 20 3433 3372 61 100 0.295 0.3064 0.361 0.3624 RANDOM 60.988
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] 2.93 1.47 2.93 -4.4
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.149 r_angle_refined_deg 3.978 r_scbond_it 2.524 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.186 r_symmetry_hbond_refined 0.166 r_bond_refined_d 0.02
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.149 r_angle_refined_deg 3.978 r_scbond_it 2.524 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.186 r_symmetry_hbond_refined 0.166 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_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_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 341 Solvent Atoms 19 Heterogen Atoms 5
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling