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Cycloalternan-forming enzyme from Listeria monocytogenes in complex with panose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 0.5 NaCl, 10 mM Tris pH 8.3, 5 mM BME
Crystallization: 200 mM magnesium formate and 25% PEG 3350
Soak for 1 minute in reservoir + 5 mM panose
Crystal Properties Matthews coefficient Solvent content 2.56 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.157 α = 90 b = 102.437 β = 103.78 c = 74.011 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 300 mm CCD Be-Lenses 2014-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.9 30 99.9 0.06 20.6 3.8 94486 -3 30.8
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 1.9 1.93 99.3 0.6 2.1 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT 4kmq 1.9 29.74 89736 4728 99.74 0.15433 0.15219 0.1665 0.19495 0.2101 RANDOM 44.394
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] 2.48 5.33 -4.81 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.063 r_dihedral_angle_4_deg 14.65 r_dihedral_angle_3_deg 10.175 r_dihedral_angle_1_deg 4.302 r_angle_refined_deg 1.682 r_angle_other_deg 0.792 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.063 r_dihedral_angle_4_deg 14.65 r_dihedral_angle_3_deg 10.175 r_dihedral_angle_1_deg 4.302 r_angle_refined_deg 1.682 r_angle_other_deg 0.792 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 8343 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing Coot model building