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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 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.438 α = 90 b = 83.438 β = 90 c = 44.776 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 1.8 20 99.9 0.068 16.3 8.2 15153
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 1.8 1.86 100 0.336 5.6 7.8
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 1.8 20 14366 767 99.9 0.14 0.138 0.1744 0.178 0.1958 RANDOM 23.41
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] -0.65 -0.65 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.063 r_scangle_it 6.336 r_scbond_it 4.437 r_mcangle_it 2.644 r_mcbond_it 1.759 r_angle_refined_deg 1.622 r_angle_other_deg 0.89 r_symmetry_hbond_refined 0.302 r_symmetry_vdw_other 0.267 r_nbd_other 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.063 r_scangle_it 6.336 r_scbond_it 4.437 r_mcangle_it 2.644 r_mcbond_it 1.759 r_angle_refined_deg 1.622 r_angle_other_deg 0.89 r_symmetry_hbond_refined 0.302 r_symmetry_vdw_other 0.267 r_nbd_other 0.262 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.196 r_metal_ion_refined 0.172 r_chiral_restr 0.11 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 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 154 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing