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N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus with substrate N,N-diacetylchitobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M ammonium chloride, 0.1M MES pH6.0, 20% v/v PEG 6000,
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.164 α = 90 b = 151.662 β = 93.33 c = 167.092 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-F 2018-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9797 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.08 48.38 99.3 0.077 14.6 6.7 72565
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 3.08 3.19 94.75 0.657 2
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 8BGN 3.08 48.38 71565 1000 99.27 0.1687 0.168 0.1725 0.2147 0.214 RANDOM 93.303
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] -3.11 -2.93 3.19 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_3_deg 15.468 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.523 r_angle_other_deg 1.199 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_3_deg 15.468 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.523 r_angle_other_deg 1.199 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26314 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 360
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Coot model building PHASER phasing REFMAC refinement