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Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae in a catalytically competent conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 100 mM Hepes pH 7.5, 50 mM Cadmium sulfate and 1 M of Sodium acetate, soaked with 20 mM EDTA
Crystal Properties Matthews coefficient Solvent content 2.19 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.111 α = 90 b = 57.111 β = 90 c = 32.674 γ = 120
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 2023-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.5 28.56 99.3 0.223 0.109 0.986 6.1 10.2 18946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.1 1.759 0.864 0.715 1.3 10.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 28.556 18928 912 99.131 0.167 0.1655 0.1626 0.1987 0.1962 29.239
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] -15.593 -15.593 31.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.822 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_2_deg 6.965 r_dihedral_angle_1_deg 6.257 r_lrange_it 5.502 r_lrange_other 5.173 r_mcangle_it 2.175 r_mcangle_other 2.173 r_scangle_it 1.755 r_scangle_other 1.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.822 r_dihedral_angle_3_deg 12.987 r_dihedral_angle_2_deg 6.965 r_dihedral_angle_1_deg 6.257 r_lrange_it 5.502 r_lrange_other 5.173 r_mcangle_it 2.175 r_mcangle_other 2.173 r_scangle_it 1.755 r_scangle_other 1.754 r_mcbond_it 1.298 r_mcbond_other 1.292 r_scbond_it 1.044 r_scbond_other 1.042 r_angle_refined_deg 1.008 r_angle_other_deg 0.379 r_symmetry_xyhbond_nbd_refined 0.294 r_symmetry_nbd_refined 0.271 r_symmetry_metal_ion_refined 0.27 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.199 r_nbd_refined 0.187 r_nbtor_refined 0.176 r_nbd_other 0.133 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.053 r_chiral_restr 0.05 r_metal_ion_refined 0.027 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 894 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing