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Structure of the alginate epimerase/lyase complexed with di-mannuronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.15-0.25M calcium chloride, 16-22% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.33 α = 90 b = 40.03 β = 91.45 c = 188.29 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2022-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.82 47.06 98.29 0.1873 0.199 0.0647 0.986 8.41 8 80215
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.885 90.32 0.3867 0.428 0.1763 0.78 2.29 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.82 47.06 1.65 80215 4307 98.31 0.2242 0.2166 0.2436 0.2538 16.13
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.9687 f_angle_d 0.6094 f_chiral_restr 0.047 f_plane_restr 0.0138 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7196 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing