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Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with Gal-PUGNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Na-citrate, PEG 2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.439 α = 90 b = 102.626 β = 90 c = 108.236 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 225 mm CCD 2010-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 50 0.097 7.5 70177
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 0.374 7.4
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 3GH4 1.6 50 66605 3538 99.99 0.14523 0.14394 0.1437 0.16915 0.1697 RANDOM 10.779
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] -0.14 -0.02 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 15.561 r_dihedral_angle_3_deg 11.944 r_dihedral_angle_1_deg 5.598 r_sphericity_free 2.716 r_scangle_it 2.551 r_scbond_it 1.683 r_sphericity_bonded 1.545 r_angle_refined_deg 1.231 r_mcangle_it 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 15.561 r_dihedral_angle_3_deg 11.944 r_dihedral_angle_1_deg 5.598 r_sphericity_free 2.716 r_scangle_it 2.551 r_scbond_it 1.683 r_sphericity_bonded 1.545 r_angle_refined_deg 1.231 r_mcangle_it 1.071 r_rigid_bond_restr 0.935 r_mcbond_it 0.685 r_nbtor_refined 0.311 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling