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3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBC PDB ENTRY 1NBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4000
Crystal Properties Matthews coefficient Solvent content 3.52 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.129 α = 90 b = 74.129 β = 90 c = 82.501 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 100 CCD ADSC CCD 2004-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.3 50 94.6 0.07 48.1 8.1 57111 17.1
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 1.3 1.35 81.5 0.52 1.86 7.6
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 1NBC 1.31 20 50547 2700 94.51 0.12127 0.11951 0.1346 0.15439 0.1642 RANDOM 16.301
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] 0.25 0.25 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.02 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 11.166 r_scangle_it 10.245 r_dihedral_angle_1_deg 7.36 r_scbond_it 7.234 r_mcangle_it 5.203 r_mcbond_it 3.938 r_rigid_bond_restr 2.8 r_angle_refined_deg 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.02 r_dihedral_angle_4_deg 18.519 r_dihedral_angle_3_deg 11.166 r_scangle_it 10.245 r_dihedral_angle_1_deg 7.36 r_scbond_it 7.234 r_mcangle_it 5.203 r_mcbond_it 3.938 r_rigid_bond_restr 2.8 r_angle_refined_deg 2.044 r_angle_other_deg 1.543 r_mcbond_other 1.169 r_chiral_restr 0.138 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing