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Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GSL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 308 0.1M SPG buffer pH 8.0, 25% v/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.4 α = 90 b = 120.5 β = 90 c = 145.6 γ = 90
Symmetry Space Group C 2 2 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 2020-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 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 2.1 50 99.5 0.111 19.43 11.5 46003
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 2.1 2.23 0.839
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 46.42 44987 998 99.58 0.1662 0.165 0.18 0.2193 0.2272 RANDOM 47.76
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] -0.51 2.2 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.431 r_dihedral_angle_4_deg 20.951 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_1_deg 9.161 r_angle_refined_deg 1.713 r_angle_other_deg 1.335 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.431 r_dihedral_angle_4_deg 20.951 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_1_deg 9.161 r_angle_refined_deg 1.713 r_angle_other_deg 1.335 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6445 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing