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A glycoside hydrolase mutant with an unreacted activity based probe bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 12 mg/mL protein stock in mixed 1:1 with 1.2 M NaH2PO4/K2HPO4 (1:9 v/v) at 293 K.
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.17 α = 90 b = 45.12 β = 115.11 c = 82.04 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2015-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.24 28.88 89.8 0.998 13.7 3.9 126454
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 3VYO 1.24 28.88 120177 6276 89.59 0.13084 0.12933 0.1292 0.16028 0.1599 RANDOM 18.698
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] 0.28 1.26 -1.49 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.355 r_sphericity_free 32.156 r_sphericity_bonded 13.297 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_4_deg 11.594 r_dihedral_angle_1_deg 5.798 r_long_range_B_refined 4.344 r_long_range_B_other 4.344 r_scangle_other 3.397 r_scbond_it 2.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.355 r_sphericity_free 32.156 r_sphericity_bonded 13.297 r_dihedral_angle_3_deg 11.838 r_dihedral_angle_4_deg 11.594 r_dihedral_angle_1_deg 5.798 r_long_range_B_refined 4.344 r_long_range_B_other 4.344 r_scangle_other 3.397 r_scbond_it 2.837 r_scbond_other 2.834 r_rigid_bond_restr 2.685 r_mcangle_other 2.43 r_mcangle_it 2.429 r_mcbond_it 1.953 r_mcbond_other 1.953 r_angle_refined_deg 1.734 r_angle_other_deg 1.059 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3457 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing