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Crystal structure of the beta-N-acetylglucosaminidase from Thermotoga maritima
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 63.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.457 α = 90 b = 133.457 β = 90 c = 142.33 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 315r M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.90000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.43 54833
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.43 26.56 54833 48565 2572 91.98 0.1962 0.19352 0.24634 0.2295 RANDOM 51.249
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 23.078 r_dihedral_angle_3_deg 20.381 r_long_range_B_other 9.482 r_long_range_B_refined 9.481 r_scangle_other 6.808 r_dihedral_angle_1_deg 6.35 r_mcangle_other 6.242 r_mcangle_it 6.241 r_scbond_it 4.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 23.078 r_dihedral_angle_3_deg 20.381 r_long_range_B_other 9.482 r_long_range_B_refined 9.481 r_scangle_other 6.808 r_dihedral_angle_1_deg 6.35 r_mcangle_other 6.242 r_mcangle_it 6.241 r_scbond_it 4.268 r_scbond_other 4.267 r_mcbond_it 3.973 r_mcbond_other 3.962 r_angle_other_deg 2.352 r_angle_refined_deg 1.736 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 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 7089 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement