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Crystal structure of GTB C80S/C196S/C209S + UDP + 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 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.104 α = 90 b = 150.41 β = 90 c = 79.253 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) 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 2.2 20 95.8 22845 15.2
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 2.2 19.87 14568 796 94.74 0.17729 0.17451 0.1713 0.22808 0.2269 RANDOM 27.628
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 19.849 r_dihedral_angle_3_deg 15.945 r_dihedral_angle_1_deg 7.381 r_scangle_it 4.794 r_scbond_it 3.051 r_angle_refined_deg 2.202 r_mcangle_it 1.973 r_mcbond_it 1.087 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.854 r_dihedral_angle_4_deg 19.849 r_dihedral_angle_3_deg 15.945 r_dihedral_angle_1_deg 7.381 r_scangle_it 4.794 r_scbond_it 3.051 r_angle_refined_deg 2.202 r_mcangle_it 1.973 r_mcbond_it 1.087 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.211 r_chiral_restr 0.2 r_xyhbond_nbd_refined 0.187 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 2192 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 53
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction