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GH20C, Beta-hexosaminidase from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EPN PDB ENTRY 2EPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10.2 12% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.84 α = 90 b = 136.94 β = 90 c = 202.35 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 291 CCD RIGAKU R-AXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002
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 1.94 50.7 97.4 0.11 9.2 3.8 184285 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 1.94 2.05 96.9 0.34 3.9 3.7
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 2EPN 1.94 113.41 174931 9269 97.22 0.20853 0.20591 0.2145 0.2579 0.2639 RANDOM 19.831
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] 0.82 -1.32 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 16.946 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.228 r_mcangle_it 1.594 r_angle_refined_deg 1.283 r_scbond_it 1.022 r_mcbond_it 0.977 r_mcbond_other 0.977 r_angle_other_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 16.946 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.228 r_mcangle_it 1.594 r_angle_refined_deg 1.283 r_scbond_it 1.022 r_mcbond_it 0.977 r_mcbond_other 0.977 r_angle_other_deg 0.792 r_chiral_restr 0.075 r_bond_refined_d 0.009 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_mcangle_other r_scbond_other r_scangle_it 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 19496 Nucleic Acid Atoms Solvent Atoms 1619 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing