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Crystal structure of unsaturated glucuronyl hydrolase mutant D175N from Streptcoccus agalactiae
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% PEG 3000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.117 α = 90 b = 53.372 β = 96.51 c = 70.165 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 2009-06-30 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 2.5 30 99 0.064 3.7 13575
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) 2.5 2.59 98.4 0.352 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2.5 29.16 12911 12769 657 98.9 0.19039 0.18709 0.1836 0.26002 0.2538 RANDOM 35.806
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] -0.24 1.45 0.21 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.879 r_dihedral_angle_4_deg 18.917 r_dihedral_angle_3_deg 15.261 r_dihedral_angle_1_deg 5.244 r_scangle_it 1.456 r_angle_refined_deg 1.002 r_scbond_it 0.871 r_mcangle_it 0.824 r_mcbond_it 0.445 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.879 r_dihedral_angle_4_deg 18.917 r_dihedral_angle_3_deg 15.261 r_dihedral_angle_1_deg 5.244 r_scangle_it 1.456 r_angle_refined_deg 1.002 r_scbond_it 0.871 r_mcangle_it 0.824 r_mcbond_it 0.445 r_chiral_restr 0.081 r_bond_refined_d 0.008 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 3127 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling