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alpha-glucan recognition by a family 41 carbohydrate-binding module from Thermotoga maritima pullulanase PulA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J71 PDB ENTRY 2J71
Crystallization Crystal Properties Matthews coefficient Solvent content 1.71 27.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.429 α = 90 b = 37.179 β = 112.38 c = 57.213 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 113 IMAGE PLATE RIGAKU IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.49 19.81 97.5 0.06 11.9 3.97 33245 2
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 1.49 1.54 94.5 0.4 2.8 3.37
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 2J71 1.49 52.7 31569 1675 97.4 0.168 0.165 0.1744 0.232 0.239 RANDOM 16.68
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] -0.25 -0.02 -0.47 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 16.97 r_scangle_it 4.555 r_scbond_it 3.251 r_mcangle_it 2.351 r_angle_refined_deg 1.944 r_mcbond_it 1.65 r_angle_other_deg 0.873 r_symmetry_vdw_refined 0.319 r_symmetry_vdw_other 0.285 r_symmetry_hbond_refined 0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 16.97 r_scangle_it 4.555 r_scbond_it 3.251 r_mcangle_it 2.351 r_angle_refined_deg 1.944 r_mcbond_it 1.65 r_angle_other_deg 0.873 r_symmetry_vdw_refined 0.319 r_symmetry_vdw_other 0.285 r_symmetry_hbond_refined 0.271 r_nbd_other 0.261 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.119 r_nbtor_other 0.089 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 1703 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement MOLREP phasing