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Exo-beta-D-glucosaminidase from Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% MPD, 100 mM Tris pH 8.5, 500 mM Sodium chloride, 8% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.13 α = 90 b = 149.597 β = 102.07 c = 147.315 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 173 CCD RAYONIX MX300HE 2016-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 50 98.4 0.091 0.1 0.038 10.9 5.2 356244
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 96 0.444 0.523 0.27 0.17 3.2
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 5GSM 1.75 30 338231 17963 98.03 0.15161 0.14797 0.1545 0.21995 0.2286 RANDOM 34.453
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] 2.36 2.73 -4.45 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 19.095 r_dihedral_angle_3_deg 17.072 r_rigid_bond_restr 14.128 r_long_range_B_refined 8.449 r_long_range_B_other 8.391 r_scangle_other 8.1 r_dihedral_angle_1_deg 7.511 r_scbond_it 7.113 r_scbond_other 7.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.13 r_dihedral_angle_4_deg 19.095 r_dihedral_angle_3_deg 17.072 r_rigid_bond_restr 14.128 r_long_range_B_refined 8.449 r_long_range_B_other 8.391 r_scangle_other 8.1 r_dihedral_angle_1_deg 7.511 r_scbond_it 7.113 r_scbond_other 7.113 r_mcangle_it 6.804 r_mcangle_other 6.804 r_mcbond_it 5.758 r_mcbond_other 5.755 r_angle_refined_deg 1.862 r_angle_other_deg 1.66 r_chiral_restr 0.093 r_bond_other_d 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25252 Nucleic Acid Atoms Solvent Atoms 1956 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing PHENIX model building HKL-2000 data reduction