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CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X2H PDB ENTRY 2X2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.643 α = 80.38 b = 97.008 β = 83.11 c = 135.708 γ = 85.22
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 315r 2010-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.1 47.7 96 0.11 5.1 1.9 255868 -3 24.8
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 2.1 2.21 92.3 0.48 1.4 1.7
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2X2H 2.1 46.74 242819 12914 95.95 0.22263 0.22022 0.2219 0.26742 0.267 RANDOM 35.721
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] -2.73 0.03 -0.03 -0.48 2.47 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_1_deg 8.798 r_scangle_it 1.993 r_scbond_it 1.36 r_angle_refined_deg 1.294 r_mcangle_it 0.805 r_mcbond_it 0.459 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_4_deg 17.765 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_1_deg 8.798 r_scangle_it 1.993 r_scbond_it 1.36 r_angle_refined_deg 1.294 r_mcangle_it 0.805 r_mcbond_it 0.459 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other 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 32648 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling