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Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing three zinc atoms at the binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other C-TERMINAL DOMAIN OF SPR1875 CONTAINING FOUR ZINC ATOMS
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, 1 M SODIUM ACETATE, 5 MM EDTA
Crystal Properties Matthews coefficient Solvent content 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.192 α = 90 b = 57.192 β = 90 c = 32.506 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 2019-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.2837 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 1.6 28.6 99.7 0.144 0.144 7.4 8.9 15644 26.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.381 0.8 9.8
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 C-TERMINAL DOMAIN OF SPR1875 CONTAINING FOUR ZINC
ATOMS 1.6 28.6 15643 741 99.7 0.218 0.2195 0.254 0.2461 30.17
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] -12.39 -12.39 24.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.289 r_dihedral_angle_4_deg 19.001 r_dihedral_angle_3_deg 15.008 r_dihedral_angle_1_deg 6.566 r_scangle_it 3.459 r_scangle_other 3.456 r_mcangle_it 3.288 r_mcangle_other 3.286 r_scbond_it 2.748 r_scbond_other 2.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.289 r_dihedral_angle_4_deg 19.001 r_dihedral_angle_3_deg 15.008 r_dihedral_angle_1_deg 6.566 r_scangle_it 3.459 r_scangle_other 3.456 r_mcangle_it 3.288 r_mcangle_other 3.286 r_scbond_it 2.748 r_scbond_other 2.674 r_mcbond_it 2.194 r_mcbond_other 2.187 r_angle_refined_deg 1.76 r_angle_other_deg 1.2 r_nbd_refined 0.187 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.156 r_nbd_other 0.133 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 851 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 9
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement