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Lepidopteran-specific toxin Cry1Ac in complex with receptor specificity determinant GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ARX CHAIN A OF PDB ENTRY 4ARX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 9.8 MICRODIALYSIS AGAINST 68-70 MM REMARK 280 PIPERAZINE PH 9.8, 28-30 MM NABR, 20-22% GLYCEROL, 9% MPD, 0.5% GALNAC. FOR DETAILS SEE REFERENCE IN REMARK 1
Crystal Properties Matthews coefficient Solvent content 2.4 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.36 α = 90 b = 51.19 β = 105.75 c = 210.65 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 1998-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 2.35 46.89 87.1 0.14 8 3.1 46706
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 2.95 3.11 59.7 0.3 2.2 1.7
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 (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 CHAIN A OF PDB ENTRY 4ARX 2.95 223.61 44352 2354 87.11 0.21669 0.21523 0.2162 0.24433 0.2445 RANDOM 41.961
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] -4.9 -0.07 7.6 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.982 r_dihedral_angle_4_deg 19.07 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 5.47 r_angle_other_deg 2.434 r_angle_refined_deg 1.232 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.982 r_dihedral_angle_4_deg 19.07 r_dihedral_angle_3_deg 13.122 r_dihedral_angle_1_deg 5.47 r_angle_other_deg 2.434 r_angle_refined_deg 1.232 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 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 18374 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing