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Glycoside hydrolase BT_1003
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKX 3WKX, 4QJY experimental model PDB 4QJY 3WKX, 4QJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% (w/v) PEG 3350 and 0.2 M potassium acetate
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.44 α = 90 b = 219.44 β = 90 c = 91.809 γ = 120
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 2015-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.775 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 109.72 100 0.133 0.992 5.2 4.9 143341 29265 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 0.954 0.339 1.5 4.9 3300
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 3WKX, 4QJY 2.5 109.72 27801 1464 99.96 0.19647 0.19411 0.1983 0.23899 0.2418 RANDOM 67.308
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] -1.55 -0.77 -1.55 5.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.428 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 7.807 r_long_range_B_refined 6.409 r_long_range_B_other 6.409 r_scangle_other 4.276 r_mcangle_it 4.158 r_mcangle_other 4.158 r_mcbond_it 2.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.428 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 7.807 r_long_range_B_refined 6.409 r_long_range_B_other 6.409 r_scangle_other 4.276 r_mcangle_it 4.158 r_mcangle_other 4.158 r_mcbond_it 2.522 r_mcbond_other 2.521 r_scbond_it 2.503 r_scbond_other 2.503 r_angle_refined_deg 1.592 r_angle_other_deg 0.975 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4792 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement