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Crystal structure of GTB C80S/C196S + DA + UDP-Gal
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 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.545 α = 90 b = 149.277 β = 90 c = 79.454 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 1.81 19.92 95.6 0.074 4.55 27621
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) 1.81 1.87 93.9 0.317 4.1 4.22
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 1.4 19.87 55954 2993 95.34 0.19624 0.19452 0.1889 0.22955 0.2222 RANDOM 18.879
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.602 r_dihedral_angle_4_deg 20.694 r_dihedral_angle_3_deg 13.225 r_dihedral_angle_1_deg 6.619 r_scangle_it 5.332 r_scbond_it 3.45 r_angle_refined_deg 2.572 r_mcangle_it 2.286 r_mcbond_it 1.429 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.602 r_dihedral_angle_4_deg 20.694 r_dihedral_angle_3_deg 13.225 r_dihedral_angle_1_deg 6.619 r_scangle_it 5.332 r_scbond_it 3.45 r_angle_refined_deg 2.572 r_mcangle_it 2.286 r_mcbond_it 1.429 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.198 r_chiral_restr 0.166 r_xyhbond_nbd_refined 0.128 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 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 2183 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 89
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction