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Hammerhead Ribozyme with 5'-5' G-G linkage: Conformational change experiment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 299D NDB entry urx057
Crystallization Crystal Properties Matthews coefficient Solvent content 6.84 82.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.689 α = 90 b = 66.689 β = 90 c = 140.528 γ = 120
Symmetry Space Group P 31 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NDB entry urx057 3 19.8 6872 744 99.3 0.24559 0.24196 0.27914 RANDOM 77.623
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] 0.19 0.09 0.19 -0.28
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.077 r_scangle_it 1.728 r_scbond_it 1.087 r_xyhbond_nbd_refined 0.212 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 872 Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SCALA data scaling CNS refinement MOSFLM data reduction CCP4 data scaling CNS phasing