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Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 10 mg/mL SGPB in 10 mM MgCl2
1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.22 61.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.286 α = 90 b = 142.286 β = 90 c = 142.286 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 210 2003-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.127 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.23 40 99 0.048 37.3 8.5 136369
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.27 90.5 0.404 3 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.23 40 129481 6842 99.03 0.11326 0.11252 0.1116 0.12713 0.126 RANDOM 10.09
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.147 r_sphericity_free 19.112 r_dihedral_angle_4_deg 18.767 r_dihedral_angle_1_deg 14.29 r_dihedral_angle_3_deg 9.685 r_scangle_it 5.581 r_angle_other_deg 4.689 r_scbond_it 4.604 r_sphericity_bonded 4.432 r_mcangle_it 3.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.147 r_sphericity_free 19.112 r_dihedral_angle_4_deg 18.767 r_dihedral_angle_1_deg 14.29 r_dihedral_angle_3_deg 9.685 r_scangle_it 5.581 r_angle_other_deg 4.689 r_scbond_it 4.604 r_sphericity_bonded 4.432 r_mcangle_it 3.231 r_rigid_bond_restr 2.866 r_mcbond_it 2.567 r_angle_refined_deg 2.414 r_mcbond_other 2.36 r_nbd_refined 0.372 r_symmetry_vdw_refined 0.33 r_symmetry_vdw_other 0.26 r_nbd_other 0.258 r_xyhbond_nbd_refined 0.214 r_nbtor_refined 0.181 r_chiral_restr 0.16 r_symmetry_hbond_refined 0.146 r_nbtor_other 0.118 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.013 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing