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The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.0M Sodium acetate trihydrate, 0.1M Sodium HEPES 7.5, 0.05M Cadmium sulfate 8/3-hydrate
Crystal Properties Matthews coefficient Solvent content 3.75 67.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.175 α = 90 b = 134.175 β = 90 c = 134.175 γ = 90
Symmetry Space Group P 43 3 2
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 RAYONIX MX300HE 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 30 99.9 0.112 0.115 0.025 41.3 20 28636
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.8 0.83 0.853 0.191 0.953 19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2 29.3 27072 1439 99.66 0.15781 0.15587 0.1685 0.19478 0.2055 RANDOM 29.55
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.846 r_long_range_B_refined 24.959 r_long_range_B_other 24.416 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 8.407 r_scangle_other 7.007 r_scbond_it 4.86 r_scbond_other 4.632 r_mcangle_other 3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.846 r_long_range_B_refined 24.959 r_long_range_B_other 24.416 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 13.408 r_dihedral_angle_1_deg 8.407 r_scangle_other 7.007 r_scbond_it 4.86 r_scbond_other 4.632 r_mcangle_other 3.7 r_mcangle_it 3.698 r_mcbond_it 2.762 r_mcbond_other 2.751 r_angle_refined_deg 2.221 r_angle_other_deg 0.99 r_chiral_restr 0.142 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1880 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing