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Crystal structure of cytotoxin 13 from Naja naja, hexagonal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 273 Sodium chloride, K/NaPhosphate,MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 74.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.331 α = 90 b = 109.331 β = 90 c = 135.77 γ = 120
Symmetry Space Group P 64 2 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 PIXEL DECTRIS EIGER X 16M 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.3 50 98.39 0.104 13.4 8.2 21512
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 2.3 2.36 0.54 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1RL5 2.302 14.9 21512 1034 98.386 0.2 0.1987 0.2026 0.2283 0.2132 39.558
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] -0.008 -0.004 -0.008 0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.632 r_dihedral_angle_2_deg 22.604 r_dihedral_angle_3_deg 19.972 r_dihedral_angle_1_deg 10.474 r_lrange_it 7.999 r_lrange_other 7.648 r_scangle_other 4.864 r_scangle_it 4.863 r_mcangle_it 3.603 r_mcangle_other 3.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.632 r_dihedral_angle_2_deg 22.604 r_dihedral_angle_3_deg 19.972 r_dihedral_angle_1_deg 10.474 r_lrange_it 7.999 r_lrange_other 7.648 r_scangle_other 4.864 r_scangle_it 4.863 r_mcangle_it 3.603 r_mcangle_other 3.602 r_scbond_other 3.052 r_scbond_it 3.048 r_mcbond_it 2.134 r_mcbond_other 2.134 r_angle_refined_deg 2.094 r_angle_other_deg 1.327 r_xyhbond_nbd_refined 0.335 r_symmetry_nbd_refined 0.325 r_nbd_refined 0.234 r_nbd_other 0.234 r_symmetry_nbd_other 0.221 r_symmetry_xyhbond_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.17 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1392 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing