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Binding sub-site dissection of a family 6 carbohydrate-binding module by X-ray crystallography and isothermal titration calorimetry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GMM PDB ENTRY 1GMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 pH 4.50
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.413 α = 90 b = 83.413 β = 90 c = 44.659 γ = 90
Symmetry Space Group P 41 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 113 IMAGE PLATE RIGAKU R-AXIS IV++ OSMIC BLUE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002
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 1.89 20 99.9 0.07 16 8.2 12433
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 1.89 1.96 100 0.354 5.2 8
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 1GMM 1.89 20 12433 662 99.9 0.132 0.13 0.1698 0.166 0.1933 RANDOM 24.18
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] -0.74 -0.74 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.54 r_scangle_it 6.126 r_scbond_it 4.251 r_mcangle_it 2.62 r_mcbond_it 1.728 r_angle_refined_deg 1.631 r_angle_other_deg 0.872 r_symmetry_hbond_refined 0.312 r_nbd_other 0.265 r_symmetry_vdw_other 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.54 r_scangle_it 6.126 r_scbond_it 4.251 r_mcangle_it 2.62 r_mcbond_it 1.728 r_angle_refined_deg 1.631 r_angle_other_deg 0.872 r_symmetry_hbond_refined 0.312 r_nbd_other 0.265 r_symmetry_vdw_other 0.246 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.174 r_metal_ion_refined 0.131 r_chiral_restr 0.109 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 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_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 986 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing