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Crystal structure of GTB C80S/C196S/C209S + UDP
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 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.065 α = 90 b = 150.173 β = 90 c = 79.77 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 1.49 19.94 96.7 0.035 4.35 49738
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) 1.49 1.54 96.7 0.397 2.8 3.56
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1LZ7 1.9 19.94 22739 1213 95.51 0.17196 0.16917 0.22574 0.2207 RANDOM 22.772
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 33.227 r_dihedral_angle_4_deg 21.915 r_dihedral_angle_3_deg 14.196 r_dihedral_angle_1_deg 6.944 r_scangle_it 5.149 r_scbond_it 3.227 r_mcangle_it 2.123 r_angle_refined_deg 1.961 r_mcbond_it 1.29 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.227 r_dihedral_angle_4_deg 21.915 r_dihedral_angle_3_deg 14.196 r_dihedral_angle_1_deg 6.944 r_scangle_it 5.149 r_scbond_it 3.227 r_mcangle_it 2.123 r_angle_refined_deg 1.961 r_mcbond_it 1.29 r_nbtor_refined 0.311 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.169 r_symmetry_hbond_refined 0.096 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 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 2216 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 25
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction