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Nano-ring of cadmium ions coordinated by nvPizza2-S16S58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.18 M magnesium chloride, 90 mM HEPES, 27% PEG 400, 10% glycerol, 30 mM cadmium chloride
Crystal Properties Matthews coefficient Solvent content 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.32 α = 90 b = 110.32 β = 90 c = 110.32 γ = 90
Symmetry Space Group I 41 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 RIGAKU SATURN A200 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.8 45 99.9 0.096 34.4 27.2 10953
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 1.8 1.83 99.6 0.485 3.1 7.3
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 1.8 45 10415 526 99.95 0.18707 0.18589 0.1937 0.20965 0.2119 RANDOM 28.325
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 30.282 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 14.602 r_long_range_B_refined 7.487 r_long_range_B_other 7.471 r_dihedral_angle_1_deg 6.891 r_scangle_other 5.857 r_mcangle_other 4.841 r_mcangle_it 4.839 r_scbond_it 4.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.282 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 14.602 r_long_range_B_refined 7.487 r_long_range_B_other 7.471 r_dihedral_angle_1_deg 6.891 r_scangle_other 5.857 r_mcangle_other 4.841 r_mcangle_it 4.839 r_scbond_it 4.028 r_scbond_other 3.973 r_mcbond_it 3.264 r_mcbond_other 3.254 r_angle_refined_deg 2.107 r_angle_other_deg 1.131 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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 596 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing