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Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi in complex with N-acetylglucosamine
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 3.69 66.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.25 α = 90 b = 129.63 β = 114.36 c = 100 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 Sym I (Observed) 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 2.5 48.02 99.4 0.12 0.99 9.71 4.7 72950
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 99.9 0.53 0.85 3.17 4.53
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 2.5 48.02 69303 3648 99.56 0.2024 0.2001 0.2055 0.2476 0.2494 RANDOM 35.901
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] 0.43 0.03 -1.19 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 17.017 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.284 r_angle_other_deg 1.086 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.809 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 17.017 r_dihedral_angle_1_deg 5.692 r_angle_refined_deg 1.284 r_angle_other_deg 1.086 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10286 Nucleic Acid Atoms Solvent Atoms 885 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing Coot model building PDB_EXTRACT data extraction XSCALE data scaling