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Catalytic domain of endo-1,4-glucanase Cel6A mutant Y73S 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 1.9 36.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.041 α = 90 b = 66.537 β = 90 c = 81.432 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 ADSC CCD SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2002-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.04 40.8 93.9 0.11 0.105 17.2 8.1 104597 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 1.04 1.1 91 0.37 0.346 4.5 6.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TML 1.04 40.82 100450 5308 93.8 0.15 0.149 0.1605 0.165 RANDOM 9.85
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.692 r_scangle_it 2.85 r_scbond_it 1.895 r_mcangle_it 1.586 r_angle_refined_deg 1.479 r_mcbond_it 0.996 r_angle_other_deg 0.92 r_nbd_other 0.249 r_nbd_refined 0.217 r_symmetry_vdw_other 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.692 r_scangle_it 2.85 r_scbond_it 1.895 r_mcangle_it 1.586 r_angle_refined_deg 1.479 r_mcbond_it 0.996 r_angle_other_deg 0.92 r_nbd_other 0.249 r_nbd_refined 0.217 r_symmetry_vdw_other 0.211 r_symmetry_vdw_refined 0.139 r_chiral_restr 0.128 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 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_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 2096 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing