☰ Navigation Tabs
Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SGR PDB ENTRY 1SGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 10 mg/mL SGPB in 10 mM MgCl2
0.7 M KH2PO4 pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.461 α = 90 b = 107.47 β = 90 c = 36.792 γ = 90
Symmetry Space Group P 21 21 2
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 2003-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.954 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 1.18 20 98.3 0.071 12.4 3.6 56646
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 1.18 1.22 91.7 0.291 3.1 2.2 5212
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 1SGR 1.18 20 53726 2869 98.3 0.14727 0.1454 0.1682 0.18204 0.2019 RANDOM 7.577
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] -0.75 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.163 r_dihedral_angle_4_deg 20.659 r_sphericity_free 15.007 r_dihedral_angle_1_deg 14.368 r_dihedral_angle_3_deg 9.374 r_scangle_it 5.267 r_sphericity_bonded 4.846 r_scbond_it 4.563 r_mcangle_it 3.423 r_mcbond_it 2.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.163 r_dihedral_angle_4_deg 20.659 r_sphericity_free 15.007 r_dihedral_angle_1_deg 14.368 r_dihedral_angle_3_deg 9.374 r_scangle_it 5.267 r_sphericity_bonded 4.846 r_scbond_it 4.563 r_mcangle_it 3.423 r_mcbond_it 2.973 r_rigid_bond_restr 2.512 r_angle_refined_deg 2.467 r_angle_other_deg 1.765 r_mcbond_other 1.543 r_symmetry_vdw_refined 0.339 r_symmetry_vdw_other 0.307 r_nbd_refined 0.232 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.184 r_chiral_restr 0.158 r_nbtor_other 0.095 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_bond_other_d 0.013 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1343 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing