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Crystal Structure of Family 7 Alginate Lyase A1-II' from Sphingomonas sp. A1
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 6.5 293 2.0M ammonium sulfate, 5% PEG 400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 32.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.335 α = 90 b = 41.329 β = 90 c = 133.378 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 mirrors 2004-12-18 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 1.6 66.67 0.068 35.4 5.4 42553 30750
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 1.6 1.66 0.197 5.7 5.4 3814
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 1.6 66.67 23016 1207 93.25 0.17863 0.17665 0.1763 0.21754 0.2177 RANDOM 15.625
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] -0.07 0.76 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.724 r_dihedral_angle_4_deg 14.393 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 6.895 r_scangle_it 2.866 r_scbond_it 2.119 r_angle_refined_deg 1.333 r_mcangle_it 1.235 r_mcbond_it 0.727 r_symmetry_hbond_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.724 r_dihedral_angle_4_deg 14.393 r_dihedral_angle_3_deg 14.178 r_dihedral_angle_1_deg 6.895 r_scangle_it 2.866 r_scbond_it 2.119 r_angle_refined_deg 1.333 r_mcangle_it 1.235 r_mcbond_it 0.727 r_symmetry_hbond_refined 0.322 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.265 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.097 r_bond_refined_d 0.01 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 1786 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing