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Inactive D62N mutant of BT1760 Endo-acting levanase from Bacteroides thetaiotaomicron VPI-5482
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1.5 M lithium sulfate, 100 mM Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.47 64.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.72 α = 90 b = 174.72 β = 90 c = 215.59 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2009-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97630 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 2.65 67.87 99.9 0.997 12.1 16.3 48504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 0.911 0.708 15.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.65 67.87 48484 2381 99.916 0.194 0.1914 0.1914 0.246 0.2458 59.916
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] 3.516 3.516 -7.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.922 r_dihedral_angle_6_deg 15.413 r_lrange_it 10.92 r_lrange_other 10.92 r_dihedral_angle_2_deg 9.792 r_scangle_it 9.664 r_scangle_other 9.239 r_dihedral_angle_1_deg 8.202 r_mcangle_it 7.828 r_mcangle_other 7.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.922 r_dihedral_angle_6_deg 15.413 r_lrange_it 10.92 r_lrange_other 10.92 r_dihedral_angle_2_deg 9.792 r_scangle_it 9.664 r_scangle_other 9.239 r_dihedral_angle_1_deg 8.202 r_mcangle_it 7.828 r_mcangle_other 7.828 r_scbond_it 7.123 r_scbond_other 6.855 r_mcbond_it 5.77 r_mcbond_other 5.769 r_angle_refined_deg 1.991 r_angle_other_deg 0.588 r_symmetry_nbd_refined 0.349 r_symmetry_nbd_other 0.198 r_nbd_refined 0.195 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.17 r_nbd_other 0.147 r_symmetry_nbtor_other 0.093 r_ncsr_local_group_1 0.087 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7800 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction XDS data reduction Aimless data scaling CRANK2 phasing Coot model building MolProbity model building