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Crystal structure of catalytic domain in closed conformation of LytB from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 PEG 300
Bis-Tris
calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.157 α = 90 b = 92.675 β = 90 c = 124.56 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 1.78 43.43 99.7 0.093 0.042 11.5 5.6 26519 19.58
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 1.78 1.82 0.763 0.354
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 4Q2W 1.8 43.43 24271 1354 99.56 0.1596 0.157 0.1624 0.2072 0.184 RANDOM 24.393
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] 2.44 -1.76 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.127 r_dihedral_angle_4_deg 25.556 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 6.34 r_rigid_bond_restr 4.393 r_angle_refined_deg 1.788 r_angle_other_deg 1.473 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.127 r_dihedral_angle_4_deg 25.556 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 6.34 r_rigid_bond_restr 4.393 r_angle_refined_deg 1.788 r_angle_other_deg 1.473 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing