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Crystal structure of unsaturated glucuronyl hydrolase mutant D175N from Streptcoccus agalactiae complexed with dGlcA-GalNAc6S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 40% ethylene glycol, 5% PEG3000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.178 α = 90 b = 53.267 β = 96.58 c = 70.136 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 100 CCD ADSC QUANTUM 210 2009-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.02 20 98.4 0.071 3.8 25199
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) 2.02 2.09 97.7 0.38 3.8 2470
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 2ZZR 2.02 20 23909 1285 98.28 0.17592 0.17409 0.1707 0.20945 0.2085 RANDOM 22.738
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] 0.1 1.11 -0.27 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 5.134 r_scangle_it 2.318 r_scbond_it 1.432 r_angle_refined_deg 0.997 r_mcangle_it 0.971 r_mcbond_it 0.514 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 20.663 r_dihedral_angle_3_deg 14.58 r_dihedral_angle_1_deg 5.134 r_scangle_it 2.318 r_scbond_it 1.432 r_angle_refined_deg 0.997 r_mcangle_it 0.971 r_mcbond_it 0.514 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3118 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling