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Crystal structure of the endo-beta-1,4-glucanase Xac0029 from Xanthomonas axonopodis pv. citri
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 293 25% PEG4000
0.2 M ammonium sulfate
15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.604 α = 90 b = 85.604 β = 90 c = 84.423 γ = 120
Symmetry Space Group P 32 2 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 2015-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4587 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 1.6 42.8 99.8 0.067 15.14 7.06 47130 -3 29.143
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 1.6 1.7 99.1 0.906 1.28
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 4W7U 1.6 42.8 44754 2381 99.82 0.1682 0.1662 0.1718 0.2038 0.211 RANDOM 23.898
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] -1.12 -0.56 -1.12 3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.901 r_sphericity_free 22.833 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 12.75 r_sphericity_bonded 8.708 r_dihedral_angle_1_deg 5.86 r_mcangle_it 2.127 r_mcbond_it 1.605 r_mcbond_other 1.586 r_angle_refined_deg 1.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.901 r_sphericity_free 22.833 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_3_deg 12.75 r_sphericity_bonded 8.708 r_dihedral_angle_1_deg 5.86 r_mcangle_it 2.127 r_mcbond_it 1.605 r_mcbond_other 1.586 r_angle_refined_deg 1.306 r_rigid_bond_restr 1.169 r_angle_other_deg 0.951 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2455 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing