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Crystal structure of the C-terminal domain of VldE H373A from Streptococcus pneumoniae
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 7.2 291 100 mM Hepes pH 7.2, 50 mM Cadmium sulfate and 0.6 M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.139 α = 90 b = 59.139 β = 90 c = 32.481 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 2023-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.14 29.57 100 0.052 0.057 0.999 18.8 9.9 46365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.16 100 1.879 0.401 1.1 9.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.14 29.569 46362 2404 99.985 0.109 0.1074 0.1278 0.1485 18.184
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] -8.187 -8.187 16.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.406 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_2_deg 10.838 r_lrange_it 7.579 r_lrange_other 6.352 r_dihedral_angle_1_deg 5.833 r_scangle_it 2.73 r_scangle_other 2.728 r_mcangle_it 2.661 r_mcangle_other 2.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.406 r_dihedral_angle_3_deg 11.658 r_dihedral_angle_2_deg 10.838 r_lrange_it 7.579 r_lrange_other 6.352 r_dihedral_angle_1_deg 5.833 r_scangle_it 2.73 r_scangle_other 2.728 r_mcangle_it 2.661 r_mcangle_other 2.661 r_mcbond_it 1.737 r_scbond_it 1.729 r_mcbond_other 1.727 r_scbond_other 1.721 r_rigid_bond_restr 1.075 r_angle_refined_deg 0.979 r_angle_other_deg 0.358 r_symmetry_nbd_refined 0.25 r_symmetry_xyhbond_nbd_refined 0.211 r_nbd_refined 0.199 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.176 r_nbd_other 0.161 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 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 889 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing