☰ Navigation Tabs
Crystal structure of GTB C80S/C196S/C209S + H antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ7 PDB entry 1LZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 279.15 35mM sodium acetate pH 4.6, 45 mM ADA, 30mM sodium chloride, 3-4 mM magnesium chloride, 3-3.5% PEG 4000, vapor diffusion, hanging drop, temperature 279.15K
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.481 α = 90 b = 149.506 β = 90 c = 79.563 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue 2005-04-27 Molecular Replacement
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002
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 1.48 19.89 97.2 0.038 3.67 51095
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 1.48 1.53 99.4 0.249 4.1 3.39
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 PDB entry 1LZ7 1.48 19.22 48440 2600 97.16 0.20372 0.20194 0.1945 0.23819 0.2304 RANDOM 21.076
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.605 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_1_deg 6.546 r_scangle_it 5.166 r_scbond_it 3.366 r_mcangle_it 2.365 r_angle_refined_deg 2.178 r_mcbond_it 1.415 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.605 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_1_deg 6.546 r_scangle_it 5.166 r_scbond_it 3.366 r_mcangle_it 2.365 r_angle_refined_deg 2.178 r_mcbond_it 1.415 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.216 r_chiral_restr 0.15 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.13 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2211 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 28
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction