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Crystal structure of nigritoxine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 2 microL of protein with 1 microL of reservoir solution, containing 100 mM Bis-Tris propane buffer at pH 8.5, 24 % (w/v) PEG 3350, 0.1 M Sodium Fluorate
Crystal Properties Matthews coefficient Solvent content 3.38 63.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.16 α = 90 b = 185.16 β = 90 c = 185.16 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-03-28 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.979 SOLEIL PROXIMA 2 2 SYNCHROTRON ESRF BEAMLINE ID29 1.0332 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 58 99.2 0.052 0.032 13.3 3.4 57805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 97.7 0.33 0.21 3.3
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 SAD THROUGHOUT 2.1 58 57805 3069 99.17 0.19501 0.19333 0.1971 0.22647 0.2271 RANDOM 56.336
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 34.21 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_1_deg 5.631 r_angle_refined_deg 1.283 r_angle_other_deg 0.91 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_dihedral_angle_4_deg 17.899 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_1_deg 5.631 r_angle_refined_deg 1.283 r_angle_other_deg 0.91 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5520 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXDE phasing