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Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 12% PEG 6000, 200 MM TRIS PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.44 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.719 α = 90 b = 82.746 β = 90 c = 118.079 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 RAYONICS TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.54 25 97.1 0.06 19.3 3.6 108114 -3
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 1.54 1.6 81.6 0.35 2.6 3
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 MOLECULAR REPLACEMENT THROUGHOUT HOMOLOGY MODEL 1.54 23.93 105364 2677 97.1 0.163 0.162 0.17 0.188 0.1999 RANDOM 12.31
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 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 13.412 r_dihedral_angle_3_deg 11.123 r_dihedral_angle_1_deg 6.919 r_scangle_it 2.555 r_scbond_it 1.912 r_angle_refined_deg 1.344 r_mcangle_it 1.102 r_mcbond_it 0.984 r_angle_other_deg 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 13.412 r_dihedral_angle_3_deg 11.123 r_dihedral_angle_1_deg 6.919 r_scangle_it 2.555 r_scbond_it 1.912 r_angle_refined_deg 1.344 r_mcangle_it 1.102 r_mcbond_it 0.984 r_angle_other_deg 0.803 r_symmetry_vdw_other 0.315 r_symmetry_vdw_refined 0.226 r_nbd_other 0.194 r_nbd_refined 0.19 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.137 r_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5213 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing