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A carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjansonii in complex with cellobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1 M phosphate-citrate and 40% polyethylene glycol 300
Crystal Properties Matthews coefficient Solvent content 4.4 72.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.32 α = 90 b = 173.32 β = 90 c = 173.32 γ = 90
Symmetry Space Group I 4 3 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 PIXEL DECTRIS PILATUS 6M-F 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.000000 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.163 46.365 99.95 1 34.46 78.5 23991
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.163 2.24 0.542
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1i8u 2.163 46.365 23989 2400 99.954 0.183 0.179 0.1779 0.219 0.2188 52.546
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_2_deg 36.946 r_dihedral_angle_4_deg 22.231 r_dihedral_angle_3_deg 16.31 r_lrange_it 9.836 r_dihedral_angle_1_deg 8.442 r_scangle_it 7.995 r_mcangle_it 7.097 r_scbond_it 6.023 r_mcbond_it 5.179 r_angle_refined_deg 1.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 22.231 r_dihedral_angle_3_deg 16.31 r_lrange_it 9.836 r_dihedral_angle_1_deg 8.442 r_scangle_it 7.995 r_mcangle_it 7.097 r_scbond_it 6.023 r_mcbond_it 5.179 r_angle_refined_deg 1.715 r_nbtor_refined 0.316 r_nbd_refined 0.215 r_metal_ion_refined 0.168 r_symmetry_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.117 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1575 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PHENIX phasing