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CBM6ct from Clostridium thermocellum in complex with xylopentaose
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 4.6 20% PEG 1000, 0.2 M SODIUM ACETATE, 0.1 M ACETATE BUFFER PH4.6, pH 4.60
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.48 α = 90 b = 51.68 β = 102.78 c = 36.13 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2003-03-15 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) 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 1.6 52 99.5 0.03 16 3.4 13033
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 1.6 1.66 99.9 0.094 9.1 3.4
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 1.6 51.99 12391 640 99.4 0.182 0.18 0.1936 0.222 0.2333 RANDOM 13.52
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] 0.35 0.14 0.23 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.712 r_scangle_it 3.355 r_scbond_it 2.143 r_mcangle_it 1.849 r_angle_refined_deg 1.455 r_mcbond_it 1.058 r_angle_other_deg 0.83 r_symmetry_vdw_other 0.314 r_symmetry_hbond_refined 0.257 r_nbd_other 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.712 r_scangle_it 3.355 r_scbond_it 2.143 r_mcangle_it 1.849 r_angle_refined_deg 1.455 r_mcbond_it 1.058 r_angle_other_deg 0.83 r_symmetry_vdw_other 0.314 r_symmetry_hbond_refined 0.257 r_nbd_other 0.256 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.128 r_chiral_restr 0.095 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 931 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling AMoRE phasing