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Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCN
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 3.58 65.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.15 α = 90 b = 130.71 β = 112.99 c = 98.48 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 0.9998 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 2.37 90.66 99.4 0.146 0.159 0.994 9.93 6.811 84783 -3 44.968
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 2.37 2.43 99.1 1.087 1.173 0.841 2.21 7.051
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 3rcn 2.37 90.66 80567 4215 99.57 0.2166 0.2143 0.2224 0.2591 0.2626 RANDOM 50.287
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] 0.35 1.34 -3.19 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.922 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 5.887 r_angle_refined_deg 1.272 r_angle_other_deg 0.912 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.922 r_dihedral_angle_4_deg 17.085 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 5.887 r_angle_refined_deg 1.272 r_angle_other_deg 0.912 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10286 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction