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Structure of a Streptococcus pneumoniae family 85 glycoside hydrolase, Endo-D, in complex with NAG-thiazoline.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Reservoir: 20% (v/v) polyethylene glycol 3350, 0.2M MgCl2, 0.1M Tri-sodium citrate, pH 5.0.
Crystal Properties Matthews coefficient Solvent content 2.12 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.88 α = 90 b = 59.04 β = 110.25 c = 96.5 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 113 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.65 20 97.7 0.05 16.6 3.5 79465 2
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 1.65 1.74 95.4 0.442 2.2 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT NONE 1.65 20 79465 4184 97.5 0.149 0.147 0.1535 0.187 0.1926 RANDOM 14.6
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] -0.65 -0.52 0.69 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 12.745 r_dihedral_angle_3_deg 12.201 r_sphericity_free 7.254 r_dihedral_angle_1_deg 6.734 r_scangle_it 4.206 r_scbond_it 3.182 r_sphericity_bonded 2.431 r_rigid_bond_restr 2.153 r_mcangle_it 2.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.949 r_dihedral_angle_4_deg 12.745 r_dihedral_angle_3_deg 12.201 r_sphericity_free 7.254 r_dihedral_angle_1_deg 6.734 r_scangle_it 4.206 r_scbond_it 3.182 r_sphericity_bonded 2.431 r_rigid_bond_restr 2.153 r_mcangle_it 2.029 r_mcbond_it 1.604 r_angle_refined_deg 1.55 r_angle_other_deg 0.928 r_mcbond_other 0.58 r_symmetry_vdw_refined 0.418 r_symmetry_vdw_other 0.219 r_nbd_refined 0.215 r_nbd_other 0.208 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.101 r_nbtor_other 0.087 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5071 Nucleic Acid Atoms Solvent Atoms 935 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement