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Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing two zinc atoms at the binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other SPR1875 C-TERMINAL DOMAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 100 mM TRIS-HCL, pH 8.5, 50 mM CADMIUM SULFATE, 1 M SODIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.121 α = 90 b = 59.121 β = 90 c = 32.676 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 2019-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.28 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 32.68 94.8 0.151 0.151 8.9 9.7 10367 21.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.85 100 1.308 1.308 1.3 10
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE SPR1875 C-TERMINAL DOMAIN 1.85 15 10346 470 94.6 0.213 0.2179 0.258 0.2563 34.56
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] 0.31 0.155 0.31 -1.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.257 r_dihedral_angle_4_deg 30.184 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 6.723 r_scangle_it 5.799 r_scangle_other 5.798 r_mcangle_it 4.706 r_mcangle_other 4.703 r_scbond_it 4.324 r_scbond_other 4.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.257 r_dihedral_angle_4_deg 30.184 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 6.723 r_scangle_it 5.799 r_scangle_other 5.798 r_mcangle_it 4.706 r_mcangle_other 4.703 r_scbond_it 4.324 r_scbond_other 4.252 r_mcbond_it 3.151 r_mcbond_other 3.141 r_angle_refined_deg 1.672 r_angle_other_deg 1.287 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.184 r_nbtor_refined 0.16 r_nbd_other 0.115 r_metal_ion_refined 0.099 r_chiral_restr 0.072 r_symmetry_metal_ion_refined 0.038 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 862 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement