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Crystal structure of the Dimeric 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 2.43 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.63 α = 90 b = 76.38 β = 90 c = 106.87 γ = 90
Symmetry Space Group P 2 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 I04-1 0.9795 Diamond I04-1
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 2.109 50.63 91.9 0.108 0.148 0.1 0.993 7.7 3.3 22371
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 2.11 2.17 0.88 1.197 0.806 0.365 3
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 2.109 45.797 22358 1055 90.934 0.224 0.2206 0.2231 0.2962 0.3013 36.116
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] 1.529 -0.605 -0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.866 r_dihedral_angle_3_deg 17.368 r_dihedral_angle_1_deg 9.808 r_lrange_it 4.273 r_lrange_other 4.242 r_scangle_it 2.284 r_scangle_other 2.284 r_mcangle_it 2.1 r_mcangle_other 2.1 r_angle_refined_deg 1.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.866 r_dihedral_angle_3_deg 17.368 r_dihedral_angle_1_deg 9.808 r_lrange_it 4.273 r_lrange_other 4.242 r_scangle_it 2.284 r_scangle_other 2.284 r_mcangle_it 2.1 r_mcangle_other 2.1 r_angle_refined_deg 1.938 r_scbond_it 1.373 r_scbond_other 1.372 r_angle_other_deg 1.315 r_mcbond_it 1.28 r_mcbond_other 1.279 r_symmetry_xyhbond_nbd_refined 0.244 r_nbd_other 0.242 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.205 r_symmetry_nbd_other 0.197 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_other 0.123 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing