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X-ray crystal structure of the Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae E173Q mutant reveals a TIM barrel catalytic domain and two ancillary domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.35 M KSCN, 0.1 M BIS-TRIS PROPANE (PH 6.5), 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.84 α = 90 b = 226.76 β = 90 c = 68.35 γ = 90
Symmetry Space Group P 21 21 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 CCD ORODIAL FOCUSING MIRROR 2007-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 80 99.9 0.09 23 5.7 130527 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 99.7 0.34 2.7 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT NONE 1.79 49.03 125475 6652 99.9 0.166 0.164 0.202 0.2165 RANDOM 18.14
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.727 r_dihedral_angle_4_deg 13.603 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 6.439 r_scangle_it 3.101 r_scbond_it 1.902 r_angle_refined_deg 1.248 r_mcangle_it 1.184 r_mcbond_it 0.632 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.727 r_dihedral_angle_4_deg 13.603 r_dihedral_angle_3_deg 13.081 r_dihedral_angle_1_deg 6.439 r_scangle_it 3.101 r_scbond_it 1.902 r_angle_refined_deg 1.248 r_mcangle_it 1.184 r_mcbond_it 0.632 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9685 Nucleic Acid Atoms Solvent Atoms 1500 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling autoSHARP phasing SOLOMON phasing RESOLVE phasing