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Crystal Structure of the periplasmic lyase AlgL K66A Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OZV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.275 M K2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES pH 6.9. Crystals were cryoprotected by soaking for 10 min with 2 mM mannuronate tetrasaccharide and 20% (v/v) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 1.9 35.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.736 α = 90 b = 67.496 β = 90 c = 76.216 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2015-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
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 2.5 20.305 99.3 0.098 16 10.3 10903
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 2.5 2.6 100 0.435
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OZV 2.5 20.305 10332 571 99.299 0.247 0.2461 0.2505 0.2689 0.2693 39.375
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] -0.699 1.296 -0.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.293 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_3_deg 15.638 r_lrange_it 6.771 r_lrange_other 6.771 r_dihedral_angle_1_deg 6.151 r_mcangle_other 2.495 r_mcangle_it 2.494 r_scangle_it 2.421 r_scangle_other 2.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.293 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_3_deg 15.638 r_lrange_it 6.771 r_lrange_other 6.771 r_dihedral_angle_1_deg 6.151 r_mcangle_other 2.495 r_mcangle_it 2.494 r_scangle_it 2.421 r_scangle_other 2.413 r_angle_refined_deg 1.503 r_mcbond_it 1.46 r_mcbond_other 1.451 r_scbond_it 1.395 r_scbond_other 1.393 r_angle_other_deg 1.273 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_other 0.202 r_nbd_refined 0.2 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.16 r_symmetry_nbd_refined 0.125 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing