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Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A inactive mutant from Vibrio harveyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.5 293 0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.61 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.42 α = 90 b = 129.24 β = 112.2 c = 98.36 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 6M 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97889 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.6 91.09 99.8 0.125 0.136 0.993 9.7 6.861 63617 -3 56.757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.7 0.775 0.835 0.865 2.18 7.102
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 6EZR 2.6 91.09 60437 3180 99.9 0.197 0.1949 0.2002 0.2365 0.2391 RANDOM 64.279
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] 2.04 2.04 -6.58 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.224 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 5.693 r_angle_refined_deg 1.21 r_angle_other_deg 0.907 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.224 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 5.693 r_angle_refined_deg 1.21 r_angle_other_deg 0.907 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10280 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction