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Crystal structure of exotype alginate lyase Atu3025 H531A complexed with alginate trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A0O PDB ENTRY 3A0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 17% PEG 4000, 8.5% iso-propanol, 0.085M HEPES-Na, 15% glycerol, 10mM alginate trisaccharide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.845 α = 90 b = 99.643 β = 90 c = 109.168 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 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 1.000 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 2.99 50 99.5 0.099 11.2 4.2 18590
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 2.99 3.11 99.9 0.361 4.9 4.2
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 3A0O 2.99 37.85 17479 943 99.02 0.20211 0.19888 0.2014 0.26234 0.2667 RANDOM 37.671
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] -3.36 6.5 -3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 17.305 r_dihedral_angle_1_deg 5.629 r_scangle_it 1.284 r_angle_refined_deg 1.064 r_scbond_it 0.734 r_mcangle_it 0.637 r_mcbond_it 0.347 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 17.305 r_dihedral_angle_1_deg 5.629 r_scangle_it 1.284 r_angle_refined_deg 1.064 r_scbond_it 0.734 r_mcangle_it 0.637 r_mcbond_it 0.347 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.236 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6149 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling