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Crystal structure of cytotoxin 13 from Naja naja, orthorhombic 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 VAPOR DIFFUSION 5.5 293 NaCl, sodium dihydrogen phosphate, 0.1M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.51 64.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.759 α = 90 b = 97.175 β = 90 c = 131.917 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 12M 2016-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 99.17 0.2 1.8 6.3 18995
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.63 99.6 0.89
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 2.6 14.89 17772 874 99.196 0.207 0.2049 0.2101 0.2547 0.2101 93.644
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] 0.722 -0.371 -0.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.225 r_dihedral_angle_3_deg 24.148 r_dihedral_angle_4_deg 23.606 r_lrange_it 11.11 r_lrange_other 11.109 r_dihedral_angle_1_deg 10.277 r_scangle_it 7.627 r_scangle_other 7.612 r_mcangle_it 6.952 r_mcangle_other 6.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.225 r_dihedral_angle_3_deg 24.148 r_dihedral_angle_4_deg 23.606 r_lrange_it 11.11 r_lrange_other 11.109 r_dihedral_angle_1_deg 10.277 r_scangle_it 7.627 r_scangle_other 7.612 r_mcangle_it 6.952 r_mcangle_other 6.951 r_scbond_it 4.822 r_scbond_other 4.789 r_mcbond_it 4.355 r_mcbond_other 4.353 r_angle_refined_deg 2.191 r_angle_other_deg 1.278 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.226 r_symmetry_nbd_other 0.223 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2784 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing