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N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus anomalous data
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, SITTING DROP 308 2.0M ammonium sulfate, 0.1M HEPES pH 7.5, 2% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.642 α = 90 b = 158.654 β = 90 c = 158.517 γ = 90
Symmetry Space Group P 21 21 21
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 2021-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.2815 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 2.506 45.7 97.3 0.199 11.052 12.98 129806
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.506 2.619 0.4318
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 2.51 45.7 42432 1145 63.21 0.2194 0.2183 0.2185 0.2614 0.2586 RANDOM 40.197
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] -1.1 2.42 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 15.566 r_dihedral_angle_1_deg 6.72 r_angle_refined_deg 1.449 r_angle_other_deg 1.191 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 15.566 r_dihedral_angle_1_deg 6.72 r_angle_refined_deg 1.449 r_angle_other_deg 1.191 r_chiral_restr 0.064 r_bond_refined_d 0.007 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 13088 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling XDS data reduction Coot model building PHASER phasing REFMAC refinement