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Crystal Structure of a Non-hemolytic Pneumolysin from Streptococcus pneumoniae strain ST306
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 6 MM PHOSPHOCHOLINE, 0.2 M MGCL2, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.48 α = 90 b = 84.73 β = 90 c = 214.62 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2016-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 38.29 100 0.24 0.996 10.56 11.7 23881 33.98
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 2.2 2.25 100 1.318 0.843 2.7 12.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CR6 2.2 38.29 22691 1195 99.9 0.226 0.224 0.266 0.2346 RANDOM 45.6
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] -0.17 0.12 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.532 r_dihedral_angle_4_deg 17.964 r_dihedral_angle_3_deg 15.57 r_long_range_B_refined 10.012 r_long_range_B_other 10.011 r_scangle_other 6.046 r_dihedral_angle_1_deg 5.863 r_mcangle_other 5.709 r_mcangle_it 5.708 r_angle_other_deg 3.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.532 r_dihedral_angle_4_deg 17.964 r_dihedral_angle_3_deg 15.57 r_long_range_B_refined 10.012 r_long_range_B_other 10.011 r_scangle_other 6.046 r_dihedral_angle_1_deg 5.863 r_mcangle_other 5.709 r_mcangle_it 5.708 r_angle_other_deg 3.752 r_scbond_it 3.59 r_scbond_other 3.585 r_mcbond_it 3.361 r_mcbond_other 3.357 r_angle_refined_deg 1.354 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 24
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement