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Crystal structure of the C-terminal domain of sequence-specific ribonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 278 50mM MES, 0.1M cadmium chloride, 25% PEG MME, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.71 α = 90 b = 62.71 β = 90 c = 100.51 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 ADSC QUANTUM 210 2006-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.1 50 98.6 13918 13723
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 99.1
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 2DJH 2.1 47.78 13188 13006 685 98.62 0.22359 0.22181 0.2237 0.25866 0.2582 RANDOM 32.563
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] 1.02 0.51 1.02 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.87 r_dihedral_angle_3_deg 17.187 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_1_deg 6.42 r_scangle_it 4.944 r_scbond_it 3.108 r_mcangle_it 2.295 r_angle_refined_deg 1.957 r_mcbond_it 1.295 r_chiral_restr 0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.87 r_dihedral_angle_3_deg 17.187 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_1_deg 6.42 r_scangle_it 4.944 r_scbond_it 3.108 r_mcangle_it 2.295 r_angle_refined_deg 1.957 r_mcbond_it 1.295 r_chiral_restr 0.195 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1429 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling