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Catalytic domain of endo-1,4-glucanase Cel6A mutant Y73S from Thermobifida fusca
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 35.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.043 α = 90 b = 66.188 β = 90 c = 81.046 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 1.15 38.1 100 0.06 0.057 18.7 6.9 82912 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 1.15 1.16 100 0.35 0.318 4.9 6.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TML 1.15 38.07 78766 4147 100 0.166 0.164 0.172 0.192 RANDOM 11.46
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.411 r_scangle_it 3.145 r_scbond_it 2.069 r_mcangle_it 1.6 r_angle_refined_deg 1.369 r_mcbond_it 1.014 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.254 r_nbd_other 0.251 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.411 r_scangle_it 3.145 r_scbond_it 2.069 r_mcangle_it 1.6 r_angle_refined_deg 1.369 r_mcbond_it 1.014 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.254 r_nbd_other 0.251 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.112 r_nbtor_other 0.084 r_chiral_restr 0.08 r_symmetry_vdw_refined 0.059 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 2095 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing