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Catalytic amidase domain of the major autolysin LytA from Streptococcus pneumaniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 PEG 6000 12%, 0.1M TrisHCl, LiCl 0.8M, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.44 α = 90 b = 50.44 β = 90 c = 72.61 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 CCD ADSC QUANTUM 4 2010-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97900 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.05 43.7 99 0.068 7.3 2.7 95581 95581 8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 100 0.53 1.7 2.6 14111
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.05 17.46 91206 91206 4816 99.51 0.1421 0.1421 0.14131 0.1506 0.15703 0.1658 RANDOM 9.847
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] 0.08 0.04 0.08 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.208 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 10.514 r_dihedral_angle_1_deg 6.19 r_scangle_it 3.017 r_scbond_it 1.965 r_mcangle_it 1.367 r_angle_refined_deg 1.19 r_angle_other_deg 0.847 r_mcbond_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.208 r_dihedral_angle_4_deg 16.671 r_dihedral_angle_3_deg 10.514 r_dihedral_angle_1_deg 6.19 r_scangle_it 3.017 r_scbond_it 1.965 r_mcangle_it 1.367 r_angle_refined_deg 1.19 r_angle_other_deg 0.847 r_mcbond_it 0.812 r_rigid_bond_restr 0.664 r_mcbond_other 0.192 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 5
Software Software Software Name Purpose MxCuBE data collection SHELXS phasing REFMAC refinement MOSFLM data reduction SCALA data scaling