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Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E from Streptococcus Pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288 MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.37 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.302 α = 90 b = 98.302 β = 90 c = 172.6 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2003-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS 1.54179
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 2 23.84 96.9 0.08 0.08 7.7 20 56344 56344 1.8 1.8
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) 2 2.11 96.9 0.4 0.4 1.8 21.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 23.84 2 53117 53117 2835 96.73 0.176 0.174 0.1879 0.204 0.2132 RANDOM 23.35
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 25.348 r_scangle_it 3.943 r_scbond_it 2.432 r_angle_refined_deg 2.005 r_mcangle_it 1.676 r_angle_other_deg 1.103 r_mcbond_it 0.892 r_symmetry_vdw_other 0.335 r_nbd_other 0.263 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 25.348 r_scangle_it 3.943 r_scbond_it 2.432 r_angle_refined_deg 2.005 r_mcangle_it 1.676 r_angle_other_deg 1.103 r_mcbond_it 0.892 r_symmetry_vdw_other 0.335 r_nbd_other 0.263 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.139 r_symmetry_hbond_refined 0.099 r_symmetry_vdw_refined 0.096 r_nbtor_other 0.092 r_metal_ion_refined 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.006 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4940 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 30
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing