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Crystal structure of chlorotoxin, a glioma specific scorpion toxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 M monosodium phosphate and 0.75 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 1.55 20.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 22.335 α = 90 b = 26.008 β = 90 c = 47.23 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315r 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
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 1.15 30 99.7 0.04 51.1 5.5 10293
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 1.15 1.19 0.09
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 THROUGHOUT 1CHL 1.15 23.615 10253 511 99.66 0.145 0.1445 0.1519 0.1574 0.1627 6.327
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] 0.086 0.082 -0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_3_deg 9.325 r_dihedral_angle_1_deg 8.359 r_dihedral_angle_4_deg 5.777 r_angle_other_deg 1.528 r_angle_refined_deg 1.451 r_lrange_it 1.01 r_lrange_other 0.909 r_rigid_bond_restr 0.87 r_scangle_it 0.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.437 r_dihedral_angle_3_deg 9.325 r_dihedral_angle_1_deg 8.359 r_dihedral_angle_4_deg 5.777 r_angle_other_deg 1.528 r_angle_refined_deg 1.451 r_lrange_it 1.01 r_lrange_other 0.909 r_rigid_bond_restr 0.87 r_scangle_it 0.662 r_scangle_other 0.662 r_scbond_it 0.561 r_scbond_other 0.545 r_mcangle_it 0.397 r_mcangle_other 0.396 r_mcbond_it 0.293 r_mcbond_other 0.273 r_nbd_refined 0.211 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.176 r_nbtor_refined 0.166 r_nbd_other 0.161 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_refined 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 274 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing