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3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum, in-house data
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 1.8 M AMMONIUM SULFATE, 0.1 M CITRIC ACID PH 5.0
Crystal Properties Matthews coefficient Solvent content 3.41 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.897 α = 90 b = 73.897 β = 90 c = 85.755 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 IMAGE PLATE RIGAKU RAXIS-IV OSMIC CONFOCAL MIRRORS 2004-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.79 30 100 0.06 32.2 6.5 23006 22.8
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 1.79 1.85 100 0.76 32.2 6.5
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 1.85 55.98 19775 1063 99.55 0.15037 0.1482 0.1571 0.19138 0.2014 RANDOM 26.213
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] 0.61 0.61 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_4_deg 24.502 r_dihedral_angle_3_deg 16.929 r_scangle_it 10.478 r_dihedral_angle_1_deg 7.645 r_scbond_it 6.66 r_mcangle_it 5.156 r_mcbond_it 3.118 r_angle_refined_deg 1.978 r_angle_other_deg 1.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_4_deg 24.502 r_dihedral_angle_3_deg 16.929 r_scangle_it 10.478 r_dihedral_angle_1_deg 7.645 r_scbond_it 6.66 r_mcangle_it 5.156 r_mcbond_it 3.118 r_angle_refined_deg 1.978 r_angle_other_deg 1.224 r_mcbond_other 0.904 r_chiral_restr 0.13 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1210 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing