☰ Navigation Tabs
Glycoside hydrolase BT_1002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKX 3WKX and 4QJY experimental model PDB 4QJY 3WKX and 4QJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 10% (w/v) PEG 3350, 0.1 M Hepes pH 7.5 and 0.2 M L-Proline
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.23 α = 90 b = 133.238 β = 97.67 c = 224.077 γ = 90
Symmetry Space Group I 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 PILATUS 6M 2015-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 49.16 99.8 0.072 0.997 9.8 3.9 406952 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 2.03 70.8 0.914 0.708 1.4 3.6
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 and 4QJY 2 49.16 386565 20382 99.79 0.18462 0.18252 0.1902 0.22397 0.2288 RANDOM 38.635
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] -0.33 -1.06 3.75 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 7.313 r_long_range_B_refined 5.775 r_long_range_B_other 5.734 r_scangle_other 4.435 r_mcangle_it 3.407 r_mcangle_other 3.406 r_scbond_it 2.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.832 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 7.313 r_long_range_B_refined 5.775 r_long_range_B_other 5.734 r_scangle_other 4.435 r_mcangle_it 3.407 r_mcangle_other 3.406 r_scbond_it 2.948 r_scbond_other 2.948 r_mcbond_it 2.454 r_mcbond_other 2.454 r_angle_refined_deg 1.634 r_angle_other_deg 0.991 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 38322 Nucleic Acid Atoms Solvent Atoms 2771 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction Aimless data scaling Coot model building REFMAC refinement PHASER phasing