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Crystal structure of the endo-beta-1,4-glucanase (Xac0030) from Xanthomonas axonopodis pv. citri with the triple mutation His174Trp, Tyr211Ala and Lys227Arg.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 32% PEG4000
0.2 M sodium chloride
0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.554 α = 90 b = 76.87 β = 98.7 c = 128.942 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2014-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
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 1.63 41.48 93.8 0.044 15.05 2.78 110097 -3 20.272
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 1.63 1.73 83.6 0.307 2.31
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4W7U 1.63 41.47 104633 5522 93.82 0.1488 0.1462 0.1976 0.2005 RANDOM 21.303
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] 0.07 -0.08 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_sphericity_free 28.163 r_dihedral_angle_4_deg 19.737 r_dihedral_angle_3_deg 13.289 r_sphericity_bonded 8.581 r_dihedral_angle_1_deg 6.137 r_mcangle_it 2.243 r_mcbond_it 1.732 r_mcbond_other 1.729 r_angle_refined_deg 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.233 r_sphericity_free 28.163 r_dihedral_angle_4_deg 19.737 r_dihedral_angle_3_deg 13.289 r_sphericity_bonded 8.581 r_dihedral_angle_1_deg 6.137 r_mcangle_it 2.243 r_mcbond_it 1.732 r_mcbond_other 1.729 r_angle_refined_deg 1.33 r_rigid_bond_restr 1.272 r_angle_other_deg 0.943 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7408 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing