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Crystal Structure of Family 7 Alginate Lyase A1-II' Y284F in Cmplex with Product (GGG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CWS PDB ENTRY 2CWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 10% PEG 1000, 15% PEG 8000, 0.2M calcium acetate, 0.05M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.73 α = 90 b = 68.102 β = 90 c = 79.95 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 RIGAKU JUPITER 210 2006-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 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 1.65 50 97.7 0.043 56.7 6 22667
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 1.65 1.71 95.6 0.197 5.9 4.9 10515
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 2CWS 1.66 31.85 21461 1164 97.37 0.16159 0.15976 0.1596 0.19379 0.1953 RANDOM 14.75
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 -0.02 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 24.984 r_dihedral_angle_3_deg 11.181 r_dihedral_angle_1_deg 6.717 r_scangle_it 2.657 r_scbond_it 1.866 r_angle_refined_deg 1.588 r_mcangle_it 1.129 r_mcbond_it 0.721 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.555 r_dihedral_angle_4_deg 24.984 r_dihedral_angle_3_deg 11.181 r_dihedral_angle_1_deg 6.717 r_scangle_it 2.657 r_scbond_it 1.866 r_angle_refined_deg 1.588 r_mcangle_it 1.129 r_mcbond_it 0.721 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.105 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1723 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing