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Crystal Structure of pneumococcal peptidoglycan hydrolase LytB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 289 15% PEG 6000, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 289.0K
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.828 α = 90 b = 44.593 β = 94.52 c = 52.221 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2012-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97923 SSRF BL17U
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 1.65 50 98.4 0.094 0.094 14.855 5.3 34504 33952 -3 37.7
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 1.65 1.71 89.7 0.656 0.656 2.167 4.2 3070
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.65 33.1 32768 30697 1626 93.68 0.18058 0.18252 0.18058 0.21726 0.2578 RANDOM 37.7
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] 0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 12.148 r_long_range_B_refined 6.412 r_long_range_B_other 6.221 r_dihedral_angle_1_deg 5.06 r_scangle_other 3.999 r_mcangle_other 2.871 r_mcangle_it 2.87 r_scbond_it 2.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 12.148 r_long_range_B_refined 6.412 r_long_range_B_other 6.221 r_dihedral_angle_1_deg 5.06 r_scangle_other 3.999 r_mcangle_other 2.871 r_mcangle_it 2.87 r_scbond_it 2.451 r_scbond_other 2.451 r_mcbond_it 1.881 r_mcbond_other 1.875 r_angle_refined_deg 1.196 r_angle_other_deg 0.722 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 24
Software Software Software Name Purpose ADSC data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling