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Structure of D212, a nuclease from a fusselovirus.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES (PH 7.5), 0.05 M K2HPO4, 10% (W/V) PEG 8000 WITH 25% GYLCEROL AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.477 α = 90 b = 81.971 β = 115.4 c = 60.16 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD 2008-01-21 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.85, 2.06 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-1 0.77, 0.98 SSRL BL9-1
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 2.4 30 92.9 0.03 32 3.1 17143 5
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 2.4 2.49 95.7 0.33 4.3 3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIRAS THROUGHOUT NONE 2.4 29.1 17143 914 94.1 0.211 0.209 0.2149 0.245 0.2631 RANDOM 32.21
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] -0.01 -0.04 0.87 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.693 r_dihedral_angle_4_deg 14.528 r_dihedral_angle_3_deg 11.344 r_dihedral_angle_1_deg 4.531 r_scangle_it 2.842 r_scbond_it 2.331 r_angle_other_deg 2.096 r_mcbond_it 1.261 r_mcangle_it 1.239 r_angle_refined_deg 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.693 r_dihedral_angle_4_deg 14.528 r_dihedral_angle_3_deg 11.344 r_dihedral_angle_1_deg 4.531 r_scangle_it 2.842 r_scbond_it 2.331 r_angle_other_deg 2.096 r_mcbond_it 1.261 r_mcangle_it 1.239 r_angle_refined_deg 0.698 r_symmetry_hbond_refined 0.334 r_symmetry_vdw_refined 0.216 r_nbd_other 0.179 r_nbtor_refined 0.179 r_nbd_refined 0.175 r_symmetry_vdw_other 0.153 r_xyhbond_nbd_refined 0.113 r_nbtor_other 0.078 r_chiral_restr 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2811 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement