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Differential inhibition of the tandem GH20 catalytic modules in the pneumococcal exo-beta-D-N-acetylglucosaminidase, StrH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YL6 PDB ENTRY 2YL6
Crystallization Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.3 α = 90 b = 109.6 β = 90 c = 112.6 γ = 90
Symmetry Space Group I 2 2 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.36 28.81 90.1 0.07 19.1 9.8 93267 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 1.36 1.43 57.7 0.38 4 5.5
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 PDB ENTRY 2YL6 1.36 78.56 88573 4692 89.83 0.1164 0.11512 0.1235 0.13999 0.1454 RANDOM 13.024
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] 0.43 -0.22 -0.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.563 r_dihedral_angle_2_deg 35.538 r_dihedral_angle_4_deg 14.983 r_dihedral_angle_3_deg 11.421 r_sphericity_bonded 8.46 r_dihedral_angle_1_deg 5.785 r_rigid_bond_restr 3.096 r_angle_refined_deg 1.36 r_angle_other_deg 0.894 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.563 r_dihedral_angle_2_deg 35.538 r_dihedral_angle_4_deg 14.983 r_dihedral_angle_3_deg 11.421 r_sphericity_bonded 8.46 r_dihedral_angle_1_deg 5.785 r_rigid_bond_restr 3.096 r_angle_refined_deg 1.36 r_angle_other_deg 0.894 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3402 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing