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Crystal structure of the Tetrameric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 20/30/50 mg/ml Protein concentration in
0.2 Magnesium chloride hexahydrate, 0.1 M HEPES sodium salt pH 7.5. 30% v/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.65 α = 90 b = 101.14 β = 90 c = 107 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 PIXEL DECTRIS PILATUS 6M 2012-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.07 53.5 98.7 0.116 0.152 0.097 0.989 6.9 3.5 50525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.13 0.762 0.997 0.633 0.527 2.9
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 7quz 2.072 53.108 50477 2472 98.482 0.213 0.2099 0.2034 0.2706 0.2697 28.204
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] -0.185 0.611 -0.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_3_deg 15.872 r_dihedral_angle_1_deg 9.166 r_lrange_it 5.394 r_lrange_other 5.324 r_scangle_it 3.195 r_scangle_other 3.194 r_mcangle_it 2.884 r_mcangle_other 2.884 r_scbond_it 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.96 r_dihedral_angle_3_deg 15.872 r_dihedral_angle_1_deg 9.166 r_lrange_it 5.394 r_lrange_other 5.324 r_scangle_it 3.195 r_scangle_other 3.194 r_mcangle_it 2.884 r_mcangle_other 2.884 r_scbond_it 1.981 r_scbond_other 1.98 r_angle_refined_deg 1.971 r_mcbond_it 1.729 r_mcbond_other 1.729 r_angle_other_deg 1.36 r_nbd_other 0.309 r_symmetry_nbd_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_xyhbond_nbd_other 0.216 r_nbd_refined 0.204 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing