☰ Navigation Tabs
Crystal structure of catalytic domain in closed conformation of LytB (E585Q)from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 PEG 300
Bis-Tris buffer
Calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.651 α = 90 b = 92.679 β = 90 c = 124.196 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 PIXEL DECTRIS PILATUS 6M 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.25 46.34 100 0.066 0.02 20.4 12 74735 12.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 0.763 0.226
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7PJ3 1.25 43.454 74683 3754 99.973 0.137 0.136 0.1359 0.1623 0.1621 14.818
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] 0.953 -0.439 -0.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.228 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 10.828 r_rigid_bond_restr 6.124 r_dihedral_angle_1_deg 6.033 r_lrange_it 3.003 r_scangle_it 2.853 r_scangle_other 2.852 r_lrange_other 2.798 r_scbond_it 2.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.228 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 10.828 r_rigid_bond_restr 6.124 r_dihedral_angle_1_deg 6.033 r_lrange_it 3.003 r_scangle_it 2.853 r_scangle_other 2.852 r_lrange_other 2.798 r_scbond_it 2.423 r_scbond_other 2.422 r_angle_other_deg 1.765 r_angle_refined_deg 1.63 r_mcangle_other 1.514 r_mcangle_it 1.512 r_mcbond_it 1.2 r_mcbond_other 1.178 r_nbd_refined 0.222 r_nbd_other 0.215 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_other 0.16 r_metal_ion_refined 0.15 r_symmetry_metal_ion_refined 0.15 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.018 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing