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Catalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fusca in complex with methyl cellobiosyl-4-thio-beta-cellobioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TML PDB ENTRY 1TML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20-30% POLYETHYLENGLYCOL 4000 AND 0.15-0.34 M SODIUM MALONATE, PH 4.0
Crystal Properties Matthews coefficient Solvent content 2 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.317 α = 90 b = 66.815 β = 90 c = 81.187 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH SI MIRROR COATED WITH PLATINUM 2002-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 18.4 99.3 0.13 0.115 11.2 3.9 38138 6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 98.2 0.32 0.263 2.7 3.3
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 1TML 1.5 18.38 36229 1909 99.2 0.186 0.185 0.1948 0.214 0.2145 RANDOM 14.91
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.248 r_scangle_it 3.152 r_scbond_it 1.902 r_angle_refined_deg 1.421 r_mcangle_it 1.253 r_angle_other_deg 0.872 r_mcbond_it 0.689 r_nbd_other 0.246 r_symmetry_vdw_other 0.237 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.248 r_scangle_it 3.152 r_scbond_it 1.902 r_angle_refined_deg 1.421 r_mcangle_it 1.253 r_angle_other_deg 0.872 r_mcbond_it 0.689 r_nbd_other 0.246 r_symmetry_vdw_other 0.237 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.147 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.1 r_nbtor_other 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 2094 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing